NESG Wiki - User contributions [en]

Resonance Assignment/Abacus/FMCGUI objects

2010-01-09T00:23:55Z

RyanDoherty:

 
<div>Most of FMCGUI commands operate mainly with the following three objects that are loaded into computer memory: </div>
*protein sequence
*peak list
*PB fragments
<div> </div>
== '''Protein sequence''' ==
<div>The protein sequence can be loaded into the program using {[[FMCGUI commands#Data.3EProtein_Sequence.3ELoad|Data>Protein Sequence>Load ]]} or {[[FMCGUI commands#Project.3ELoad|Project>Load]]} commands. <br></div><div>The position ID of the first residue in the sequence should be specified by the user when loading the sequence file (when it is not specified in the input file). Some commands in FMCGUI assume that the first residue of the protein sequence has position ID of 1. Therefore, if there is a HIS-tag, the loaded sequence should be numbered accordingly with a negative position ID for the first residue.</div><div> </div>
== Peak list ==
<div>Different peak lists can be loaded into the program using {[[FMCGUI commands#Data.3EN15_NOESY.3E|Data>”Peak list name”>Load]]} or {[[FMCGUI commands#Project.3ELoad|Project>Load]]}</div><div></div><div></div><div><br></div>
*(+)    peak list needs to be referenced
*(+/-)  peak lists could be referenced, but it isn't necessary
*(-)     peak lists could be referenced, but it won't be used by FMCGUI<br><span>                              </span>

{| cellspacing="0" cellpadding="0" border="1"
|-
| valign="top" width="176" | <div align="center">N15 NOESY<span>              </span></div>
| valign="top" width="88" | <div align="center">-</div>
|-
| valign="top" width="176" | <div align="center">C13 NOESY H2O<span>      </span></div>
| valign="top" width="88" | <div align="center">-</div>
|-
| valign="top" width="176" | <div align="center">Arom NOESY<span>             </span></div>
| valign="top" width="88" | <div align="center">-</div>
|-
| valign="top" width="176" | <div align="center">N15 HSQC</div>
| valign="top" width="88" | <div align="center">+</div>
|-
| valign="top" width="176" | <div align="center">C13 HSQC</div>
| valign="top" width="88" | <div align="center">+</div>
|-
| valign="top" width="176" | <div align="center">HNCA</div>
| valign="top" width="88" | <div align="center">+/-</div>
|-
| valign="top" width="176" | <div align="center">HNCO</div>
| valign="top" width="88" | <div align="center">-</div>
|-
| valign="top" width="176" | <div align="center">CBCACONH</div>
| valign="top" width="88" | <div align="center">+/-</div>
|-
| valign="top" width="176" | <div align="center">HBHACONH</div>
| valign="top" width="88" | <div align="center">+</div>
|}
<div align="center"><span>           </span></div><div> </div>
== List of PB fragments ==
<div></div><div>This object can be created in memory using {[[FMCGUI commands#Fragment.3ELoad.3EPB_fragments|Fragment>Load>]]}, {[[FMCGUI commands#Fragment.3ECreate.3Eabacus|Fragment>Create>abacus]]}, or {[[FMCGUI commands#Project.3ELoad|Project>Load]]} commands. </div><div></div><div>Each PB fragment in the list has the following main properties:</div>
==== User ID       ====

     Fragment ID assigned by user, ''U_id''<span style="font-style: italic">. </span>''U_id'' can’t be changed within FMCGUI.

==== Assignment ID ====

    Assignment ID, ''A_id'',  indicates the sequence position ID to which the fragment is assigned.<br>

''A_id'' = -99 if the fragment is not assigned to any position in the sequence.

''A_id'' could be set up or modified by the following commands {[[FMCGUI commands#Assignment.3EFix_Assignment.3EManually|Assignment>Fix Assignment>Manually]]}, {[[FMCGUI commands#Assignment.3EFix_Assignment.3EUsing_Probability_map|Assignment>Fix Assignment>Using probability Map]]}, and {[[FMCGUI commands#Assignment.3EFix_Assignment.3EReset_all|Assignment>Fix Assignment>Reset all]] }.

==== Typing probabilities ====

     <span>T<sup>t </sup>(f)  </span><span>is a probability for fragment ''f ''to have amino acid type ''t''</span><span>. Here ''t ''corresponds to one of 20 amino acid residue types, and f </span><span>is fragment user ID. </span>

Typing probbilities can be calculated or modified manually by the commands {[[FMCGUI commands#Fragment.3EType.3ECalculate.3E|Fragment>Type>Calculate]]} and  {[[FMCGUI commands#Fragment.3EType.3Efix|Fragment>Type>Fix]]}, respectively.

==== Contact map ====

:There are three fragment contact maps: C<sup>f1</sup><sub>HNCA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f2'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>
<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>HNCA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>
==== Assignment probabilities ====

:  

<span>P<sup>s</sup>(f) is a probability of fragment f to be assigned to sequense position s, where f is fragment user ID, and s is sequence position ID.</span> <span>There are two assignment probabilities associated with a fragment - P<sup>s</sup><sub>SA</sub>(f) and P<sup>s</sup><sub>REM</sub>(f) - that are calculated using Simulates Annealing (SA) and </span><span>Replica Exchange Method (REM) Monte Carlo simulations, respistively.</span> <span />

<br>
<div> <span>P<sup>s</sup><sub>SA</sub>(f)    is calclated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3ESA|Assignment>Calculate Probabilities>SA]]}  </span><br></div><div>''' '''<span>P<sup>s</sup><sub>REM</sub>(f)  is calculated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3EREM|Assignment>Calculate probabilities>REM]]}.</span></div><div><br></div><div><span>Both assignment probabilities could be also  loaded in memory from already performed calculations using command {[[FMCGUI commands#Assignment.3ELoad_Probabilities|Assignment>Load probabilities]]}.</span></div><div> </div><div>'''<br>'''</div>
== Main window ==
<div></div>
==== Figure 2.1 ====
<div></div><div>[[Image:Fmcgui mainwindow.jpg|thumb|left|500px]]</div><div></div><div></div><div></div><div></div><div><br><br><br><br><br><br><br><br><br><br><br><br></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure)<br></div>
* the title bar displays the name of the current project and the directory inside which the project is located;
* the bar with six menus: [[FMCGUI commands#Project_Menu|Project]], [[FMCGUI commands#Data_Menu|Data]], [[FMCGUI commands#Fragment_menu|Fragment]], [[FMCGUI commands#Assignment_menu|Assignment]], [[FMCGUI commands#Structure_menu|Structure]], and [[FMCGUI commands#View_menu|View]], respectively;
*the project main window, where all messages from the last executed command are displayed ;
*the log window, where the history of executed commands is shown.
<div> </div><div> </div>

Resonance Assignment/Abacus/FMCGUI objects

2010-01-08T20:54:41Z

RyanDoherty:

 
<div>Most of FMCGUI commands operate mainly with the following three objects that are loaded into computer memory: </div>
*protein sequence
*peak list
*PB fragments
<div> </div>
== '''Protein sequence''' ==
<div>The protein sequence can be loaded into the program using {[[FMCGUI commands#Data.3EProtein_Sequence.3ELoad|Data>Protein Sequence>Load ]]} or {[[FMCGUI commands#Project.3ELoad|Project>Load]]} commands. <br></div><div>The position ID of the first residue in the sequence should be specified by the user when loading the sequence file (when it is not specified in the input file). Some commands in FMCGUI assume that the first residue of the protein sequence has position ID of 1. Therefore, if there is a HIS-tag, the loaded sequence should be numbered accordingly with a negative position ID for the first residue.</div><div> </div>
== Peak list ==
<div>Different peak lists can be loaded into the program using {[[FMCGUI commands#Data.3EN15_NOESY.3E|Data>”Peak list name”>Load]]} or {[[FMCGUI commands#Project.3ELoad|Project>Load]]}</div><div></div><div></div><div><br></div>
*(+)    peak list needs to be referenced
*(+/-)  peak lists could be referenced, but it isn't necessary
*(-)     peak lists could be referenced, but it won't be used by FMCGUI<br><span>                              </span>

{| cellspacing="0" cellpadding="0" border="1"
|-
| valign="top" width="176" | <div align="center">N15 NOESY<span>              </span></div>
| valign="top" width="88" | <div align="center">-</div>
|-
| valign="top" width="176" | <div align="center">C13 NOESY H2O<span>      </span></div>
| valign="top" width="88" | <div align="center">-</div>
|-
| valign="top" width="176" | <div align="center">Arom NOESY<span>             </span></div>
| valign="top" width="88" | <div align="center">-</div>
|-
| valign="top" width="176" | <div align="center">N15 HSQC</div>
| valign="top" width="88" | <div align="center">+</div>
|-
| valign="top" width="176" | <div align="center">C13 HSQC</div>
| valign="top" width="88" | <div align="center">+</div>
|-
| valign="top" width="176" | <div align="center">HNCA</div>
| valign="top" width="88" | <div align="center">+/-</div>
|-
| valign="top" width="176" | <div align="center">HNCO</div>
| valign="top" width="88" | <div align="center">-</div>
|-
| valign="top" width="176" | <div align="center">CBCACONH</div>
| valign="top" width="88" | <div align="center">+/-</div>
|-
| valign="top" width="176" | <div align="center">HBHACONH</div>
| valign="top" width="88" | <div align="center">+</div>
|}
<div align="center"><span>           </span></div><div> </div>
== List of PB fragments ==
<div></div><div>This object can be created in memory using {[[FMCGUI commands#Fragment.3ELoad.3EPB_fragments|Fragment>Load>]]}, {[[FMCGUI commands#Fragment.3ECreate.3Eabacus|Fragment>Create>abacus]]}, or {[[FMCGUI commands#Project.3ELoad|Project>Load]]} commands. </div><div></div><div>Each PB fragment in the list has the following main properties:</div>
==== User ID       ====

     Fragment ID assigned by user, ''U_id''<span style="font-style: italic">. </span>''U_id'' can’t be changed within FMCGUI.

==== Assignment ID ====

    Assignment ID, ''A_id'',  indicates the sequence position ID to which the fragment is assigned.<br>

''A_id'' = -99 if the fragment is not assigned to any position in the sequence.

''A_id'' could be set up or modified by the following commands {[[FMCGUI commands#Assignment.3EFix_Assignment.3EManually|Assignment>Fix Assignment>Manually]]}, {[[FMCGUI commands#Assignment.3EFix_Assignment.3EUsing_Probability_map|Assignment>Fix Assignment>Using probability Map]]}, and {[[FMCGUI commands#Assignment.3EFix_Assignment.3EReset_all|Assignment>Fix Assignment>Reset all]] }.

==== Typing probabilities ====

     <span>T<sup>t </sup>(f)  </span><span>is a probability for fragment ''f ''to have amino acid type ''t''</span><span>. Here ''t ''corresponds to one of 20 amino acid residue types, and f </span><span>is fragment user ID. </span>

Typing probbilities  could be calculated or modified manually by the commands {[[FMCGUI commands#Fragment.3EType.3ECalculate.3E|Fragment>Type>Calculate]]} and  {[[FMCGUI commands#Fragment.3EType.3Efix|Fragment>Type>Fix]]}, respectively.

==== Contact map ====

:There are three fragment contact maps: C<sup>f1</sup><sub>HNCA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f2'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>
<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>HNCA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>
==== Assignment probabilities ====

:  

<span>P<sup>s</sup>(f) is a probability of fragment f to be assigned to sequense position s, where f is fragment user ID, and s is sequence position ID.</span> <span>There are two assignment probabilities associated with a fragment - P<sup>s</sup><sub>SA</sub>(f) and P<sup>s</sup><sub>REM</sub>(f) - that are calculated using Simulates Annealing (SA) and </span><span>Replica Exchange Method (REM) Monte Carlo simulations, respistively.</span> <span />

<br>
<div> <span>P<sup>s</sup><sub>SA</sub>(f)    is calclated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3ESA|Assignment>Calculate Probabilities>SA]]}  </span><br></div><div>''' '''<span>P<sup>s</sup><sub>REM</sub>(f)  is calculated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3EREM|Assignment>Calculate probabilities>REM]]}.</span></div><div><br></div><div><span>Both assignment probabilities could be also  loaded in memory from already performed calculations using command {[[FMCGUI commands#Assignment.3ELoad_Probabilities|Assignment>Load probabilities]]}.</span></div><div> </div><div>'''<br>'''</div>
== Main window ==
<div></div>
==== Figure 2.1 ====
<div></div><div>[[Image:Fmcgui mainwindow.jpg|thumb|left|500px]]</div><div></div><div></div><div></div><div></div><div><br><br><br><br><br><br><br><br><br><br><br><br></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure)<br></div>
* the title bar displays the name of the current project and the directory inside which the project is located;
* the bar with six menus: [[FMCGUI commands#Project_Menu|Project]], [[FMCGUI commands#Data_Menu|Data]], [[FMCGUI commands#Fragment_menu|Fragment]], [[FMCGUI commands#Assignment_menu|Assignment]], [[FMCGUI commands#Structure_menu|Structure]], and [[FMCGUI commands#View_menu|View]], respectively;
*the project main window, where all messages from the last executed command are displayed ;
*the log window, where the history of executed commands is shown.
<div> </div><div> </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:39:28Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

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<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

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====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

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==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|center|600px]] 

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that allows the user to carry out resonance assignment and structure calculation using the ABACUS approach.  FMCGUI integrates a number of FORTRAN applications: controlling the data-flow between the applications, executing applications, and visualizing data for effective analysis of results. <br></div><div></div><div>The main purpose of FMCGUI is to provide an interactive tool for resonance assignment.  FMCGUI includes a structure calculation component, which can be used independently from the resonance assignment component.  The structure calculation component assists the user by setting up structure calculations with CYANA, water refinement calculations with CNS, and performs an analysis of their results.  The structure calculations are to be run externally from FMCGUI, on a linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:39:10Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>
<br>
 <br>

 <br>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|center|600px]] 

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that allows the user to carry out resonance assignment and structure calculation using the ABACUS approach.  FMCGUI integrates a number of FORTRAN applications: controlling the data-flow between the applications, executing applications, and visualizing data for effective analysis of results. <br></div><div></div><div>The main purpose of FMCGUI is to provide an interactive tool for resonance assignment.  FMCGUI includes a structure calculation component, which can be used independently from the resonance assignment component.  The structure calculation component assists the user by setting up structure calculations with CYANA, water refinement calculations with CNS, and performs an analysis of their results.  NOTE: The structure calculations are to be run externally from FMCGUI, on a linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:32:37Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>
<br>
 <br>

 <br>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|center|600px]] 

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that allows the user to carry out resonance assignment and structure calculation using the ABACUS approach. FMCGUI integrates a number of FORTRAN applications: controlling the data-flow between the applications, executing applications, and visualizing data for effective analysis of results. <br></div><div>The main purpose of FMCGUI is to provide an interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:28:41Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>
<br>
 <br>

 <br>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|center|600px]] 

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:28:20Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>
<br>
 <br>

 <br>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====
[[Image:Fmcgui Fig1.4.jpg|thumb|center|600px]]
<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:27:43Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>
<br>
 <br>

 <br>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====
<center>
[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]] </center>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:26:29Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

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<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>
<br>
 <br>

 <br>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

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<br>

<br>

<br>

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<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:26:08Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>

 <br>

 <br>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

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<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:25:39Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>

==== '' '' ====

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:25:23Z

RyanDoherty: /* == */

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>
====

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

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<br>

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<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:25:00Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>
</div><div></div>
 <br>
====
====

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

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<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:24:45Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

</div><div></div> <br>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:23:58Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>

<br>

 <br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:23:41Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>

</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:22:57Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (identifying neighbouring residues) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

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<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:20:32Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

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<br>

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<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

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<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:20:14Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty  S(T) scores were calculated for each spin-system ( see Figure 1.2 ).  Here ''T'' corresponds to amino acid type, and ''T ''= A, R, D, …, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:19:45Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

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</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2).  Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively.  The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database.  When the best S(T) score is low  (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

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= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:19:22Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

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<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

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====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

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</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database. When the best S(T) score is low (ie. S<sub>max </sub>< 10<sup>-4</sup>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and needs to be <span>corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

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= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Spin systems identification

2010-01-06T21:18:21Z

RyanDoherty:

<div>Normally, the NMR spectra shown in [[Introduction to ABACUS#NMR_spectra_required_for_ABACUS|Table 1]] are collected for ABCUS. Spectra should ideally be collected from the same protein preparation and under the same conditions to make sure peaks are within tolerance between spectra. All spectra need to be appropriately synchronized <span>and calibrated against reference spectra of your choice. It is a good idea to use as a reference for spectra calibration the 2D HN-projection of 15N-NOESY and the 2D CH-projection of the 13C-NOESY. </span></div><div> </div>
== Step 1. Generate HN-rooted spin-systems (''b''PB-fragments) ==

1.1[[Introduction to ABACUS#bPB_fragment|''b''PB-fragments]] can be identified using the following spectra
<div><br><span>             15N_HSQC</span></div><div><span>             HNCO</span></div><div><span>             CBCA(CO)NH</span></div><div><span>             HBHAC (CO)NH</span></div><div><span>             HNCA</span></div><div><span>            15N_NOESY</span></div><div> It is a good idea to analyze all these spectra simultaneously, for example,  using SPARKY, in order to obtain  peak lists of 15N_HSQC, HNCA,  CBCA(CO)NH, and HBHA(CO)NH spectra (see Figure 4.1A). The first two spectra should be referenced.</div><div><span> </span></div><div>'''<span> Figure 4.1A</span>'''<span>[[Image:Fmcgui Fig4.1a.jpg|thumb|center|600px]]  </span></div><div></div><div><span>        1.2. Create initial HN-rooted spin-systems (</span>[[Introduction to ABACUS#bPB_fragment|''b''PB-fragments]]<span> </span><span>) using FMCGUI:</span></div><div> </div>
*<span><span>       </span></span>start new project PRJ_1 { [[FMCGUI commands#Project.3ENew|Poject>new]] }
*<span><span>       </span></span>load protein sequence { [[FMCGUI commands#Data.3EProtein_Sequence.3ELoad|DATA>Protein Sequence>load]] }
*<span><span>       </span></span>load referenced HNCA peak list { [[FMCGUI commands#Data.3EHNCA.3E|DATA>HNCA>load]] }<br>
*<span><span>       </span></span>load referenced CBCA(CO)NH peak list { [[FMCGUI commands#Data.3ECBCACONHN.3E|DATA>CBCACONH>load]] }<br>
*<span><span>       </span></span>load referenced HBHA(CO)NH peak list { [[FMCGUI commands#Data.3EHBHACONH.3E|DATA>HBHACONH>load]] }
*<span><span>       </span></span>load referenced 15N_HSQC peak list { [[FMCGUI commands#Data.3EN15_HSQC.3E|DATA>N15 HSQC>load]] }<br>
*<span><span>       </span></span>set tolerances for matching of resonances in different spectral dimensions { [[FMCGUI commands#Data.3ETolerances|Data>Tolerances]] }<br>
*<span><span>       </span></span>create bPB-fragments { [[FMCGUI commands#Fragment.3ECreate.3Efawn|Fragment>create>fawn]] }<br>
<div>First, a referenced C13_hsqc peak list is created and shown in new window ‘fake C13 HSQC’. Warning messages are shown in the project main window. You have to check the list and modify it if needed. Then, press ‘OK’ button in the ‘‘fake C13 HSQC’ window. In the result, new window ‘Create Fragment’ pops up. The window consists of three sections. The left sections contains suggested ''b''PB-fragments, while the other sections contains two reports of fragments scoring with both C and H resonances and with only C resonances, respectively. Consider warning messages shown in the project main window and check/modify generated ''b''PB-fragments in the left section of “Create Fragment” window. When satisfied, the ''b''PB-fragments will be loaded in the memory by clicking on “OK” button.</div>
*<span>       save project PRJ_1. { [[FMCGUI commands#Project.3ESave|Project>Save]] } or  { [[FMCGUI commands#Project.3EQuit|Project>Quit]] } </span>

== Step 2. Complete PB-fragments ==

    At this step ''b''PB-fragments are completed with aliphatic side-chain resonances and  additional spin-systems (without HN) are identified using the following spectra.
<div> </div><div><span>               13C-HSQC</span></div><div>''<span>               </span>''(H)CCH-TOCSY</div><div><span>               H(C)CH-TOCSY</span> </div><div><span>               13C-NOESY</span></div><div> </div><div>        2.1. Generate expected peak lists for C13HSQC, (H)CCH-TOCSY, and H(C)CH-TOCSY spectra using created ''b''PB fragments:</div><div> </div>
*    open project PRJ1 { [[FMCGUI commands#Project.3ELoad|Project>load]] }
*    generate expected C13hsqc_exp.list that consists of C<sub>a</sub>-H<sub>a</sub> and C<sub>b</sub>-H<sub>b</sub> moieties<span>   { [[FMCGUI commands#Fragment.3EExpected_Peaks.3E|Fragment>Expected Peaks>C13HSQC]] }

</span>

*    generate expected CCH-Tocsy.list { [[FMCGUI commands#Fragment.3EExpected_Peaks.3E|Fragment>Expected Peaks>(H)CCH]] }<br>
*    generate expected HCH-Tocsy.list { [[FMCGUI commands#Fragment.3EExpected_Peaks.3E|Fragment>Expected Peaks>H(C)CH]] }<br>
<div> </div><div><span>        2.2<span>    </span></span>Read the generated peaks into SPARKY. </div><div> </div><div><span>        2.3<span>    </span></span>Using SPARKY, complete ''b''PB fragments with aliphatic side-chain resonances by analyzing C<sub>a</sub>-H<sub>a</sub> and C<sub>b</sub>-H<sub>b</sub><span> strips in all CH_rooted spectra (see Figure 4.1B,C). New resonances should be peaked and referenced ''<u>only</u>'' in 13C_HSQC spectrum.</span></div><div> </div>
=== Figure 4.1B,C ===
<div></div><div></div><div>[[Image:Fmcgui Fig4.1b.jpg|thumb|left|500px]][[Image:Fmcgui Fig4.1c.jpg|thumb|right|500px]]</div><div></div><div></div><div></div><div><span>        </span></div><div><br></div><div><span>2.4<span>    </span></span>When all peaks corresponding to HN-rooted spin-systems are peaked in 13C_HSQC spectrum, the unpicked peaks are used as a starting point for identification of spin-systems without backbone HN resonances (PB fragments corresponding to residues before prolines in the protein sequence, last residue and residues missing in HN-rooted spectra).</div><div> </div>
<br>

== Step 3. Spin-systems validation and correction ==
<div> </div><div>Validate PB-fragments using FMCGUI:</div>
*<span>        start a new project PRJ2 { [[FMCGUI commands#Project.3ENew|Project>new]] } </span>

<br>

<br>

*<span><span>        </span></span>load protein sequence { [[FMCGUI commands#Data.3EProtein_Sequence.3ELoad|DATA>Protein Sequence>load]] }
*<span><span>        </span></span>load referenced 15N_HSQC peak list { [[FMCGUI commands#Data.3EN15_HSQC.3E|DATA>N15 HSQC>load]] }
*<span><span>        </span></span>load referenced 13C_HSQC peak list { [[FMCGUI commands#Data.3EC13_HSQC.3E|DATA>C13 HSQC>load]] }
*<span><span>        </span></span>load referenced HNCA peak list { [[FMCGUI commands#Data.3EHNCA.3E|DATA>HNCA>load]] }
*<span><span>        </span></span>load  CBCA(CO)HN peak list { [[FMCGUI commands#Data.3ECBCACONHN.3E|DATA>CBCACOHN>load]] }
*<span><span>        </span></span>load  HNCO peak list { [[FMCGUI commands#Data.3EHNCO.3E|DATA>HNCO>load]] }
*<span><span>        </span></span>set tolerances for matching of resonances in different spectral dimensions  { [[FMCGUI commands#Data.3ETolerances|DATA>Tolerances]] }
*<span><span>        </span></span>create and validate PB fragments { [[FMCGUI commands#Fragment.3ECreate.3Eabacus|Fragment>create>abacus]] }
<div>This command starts script ‘''sps_create’''. In the result, a new window [[FMCGUI commands#Fragment.3ECreate.3Eabacus|"Create Fragment"]] pops up. The warning messages of the ‘''sps_create’'' script are shown in the main window and indicate spin-system that have low score (see [[Introduction to ABACUS#Figure_1.2|Figure 1.2]]), namely, spin-systems with S<sub>max</sub> < 10<sup>-4</sup>. Following the warnings check and modify, if necessary, generated PB fragments in the left section of “Create Fragment’ window. Alternatively, go back to spectra, fix peak lists accordingly, and repeat the fragment generation/validation again.</div><div>When satisfied, the PB fragments will be saved (file "sps_pb.dat" into directory "PRJ2/sps") and loaded in memory by pressing "OK" button in “Create Fragment” window.</div>
*<span>       save project PRJ2 { [[FMCGUI commands#Project.3ESave|Project>Save]] } or { [[FMCGUI commands#Project.3EQuit|Project>Quit]] } </span>

<div>''' '''</div>
<br>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T21:16:33Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

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<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

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<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts by grouping resonances into spin systems. Two types of spin-systems will be described in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragments consist of correlated resonances from the side chain of residue ''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, are called ''b''PB fragments. </span></div><div> </div><div>Spin-system identification in the ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. During the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH ) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. During the second step, completion of ''b''PB fragments with side-chain aliphatic resonances and identification of additional spin-systems (lacking HN resonances) are performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B).</div><div> </div><div>      3. During the final step, spin-system validation and correction are performed. This step allows the user to find mistakes made during spectra peak-picking and to correct the mistakes by referring back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>During the validation step, twenty S(T) scores were calculated for each spin-system (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluates goodness-of-fit for the spin-system resonances in comparison to observed data obtained from the BMRB database. When the best S(T) score is low (ie. S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)}), it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span> corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>

= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T20:46:34Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for the ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. For proteins with very few aromatic residues, collecting only one aromatic spectrum (ie. aromatic NOESY) could be sufficient for the assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>

= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment. </span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span> corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T20:40:43Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*It does not rely on sequential connectivities from less sensitive experiments (ie. HNCACB) that are indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time while “troubleshooting” NOE and resonance assignments;
*Probabilistic nature of the ABACUS procedure provides a measure of reliability for the assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) because of knowing where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment. </span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span> corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:52:44Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignment by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

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<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment. </span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span> corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

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= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:52:28Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

====                                                     ====

      

 

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment. </span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span> corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

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<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:51:55Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

==== ====

==== '''<span> </span>''' ====

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment. </span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span> corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

                                                   

  

    

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:51:30Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

==== ====

==== '''<span> </span>''' ====

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment. </span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span> corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

               

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:50:57Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

==== ====

==== '''<span> </span>''' ====

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment. </span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span> corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

=                                                          =

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:49:49Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

==== ====

==== '''<span> </span>''' ====

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| class="FCK__ShowTableBorders" cellspacing="0" cellpadding="0" border="0"
|-
| valign="top" width="197" | <div>'''NH-rooted'''</div>
| valign="top" width="197" | <div>'''CH-rooted'''</div>
| valign="top" width="197" | <div>'''Aromatic'''</div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-CT-HSQC</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HNCO</div>
| valign="top" width="197" | <div><sup>13</sup>C-HSQC</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>HNCA</div>
| valign="top" width="197" | <div>H(C)CH-TOCSY</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY-aro</div>
|-
| valign="top" width="197" | <div>CBCA(CO)NH</div>
| valign="top" width="197" | <div>(H)CCH-TOCSY</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| valign="top" width="197" | <div>HBHA(CO)NH</div>
| valign="top" width="197" | <div><sup>13</sup>C-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="197" | <div><sup>15</sup>N-NOESY-HSQC</div>
| valign="top" width="197" | <div> </div>
| valign="top" width="197" | <div> </div>
|-
| valign="top" width="590" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| valign="top" width="590" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>
==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment. </span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div><div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span> corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

=   =

= FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:48:08Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

==== ====

==== '''<span> </span>''' ====

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| cellspacing="0" cellpadding="0" border="0" class="FCK__ShowTableBorders"
|-
| width="197" valign="top" | <div>'''NH-rooted'''</div>
| width="197" valign="top" | <div>'''CH-rooted'''</div>
| width="197" valign="top" | <div>'''Aromatic'''</div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-CT-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HNCO</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>HNCA</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>CBCA(CO)NH</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HBHA(CO)NH</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
| width="197" valign="top" | <div> </div>
|-
| width="590" valign="top" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| width="590" valign="top" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span>
include all the atoms belonging to the same residue; PB-fragment
includes all the atoms from one residue except the backbone amide
group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment.
</span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div> <div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span>
corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

=  FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:47:31Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

==== ====

==== '''<span> </span>''' ====

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| cellspacing="0" cellpadding="0" border="0" class="FCK__ShowTableBorders"
|-
| width="197" valign="top" | <div>'''NH-rooted'''</div>
| width="197" valign="top" | <div>'''CH-rooted'''</div>
| width="197" valign="top" | <div>'''Aromatic'''</div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-CT-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HNCO</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>HNCA</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>CBCA(CO)NH</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HBHA(CO)NH</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
| width="197" valign="top" | <div> </div>
|-
| width="590" valign="top" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| width="590" valign="top" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span>
include all the atoms belonging to the same residue; PB-fragment
includes all the atoms from one residue except the backbone amide
group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment.
</span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div> <div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span>
corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span style="display: none;" id="1259188877701S"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

=  FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:47:21Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

==== ====

==== '''<span> </span>''' ====

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| cellspacing="0" cellpadding="0" border="0" class="FCK__ShowTableBorders"
|-
| width="197" valign="top" | <div>'''NH-rooted'''</div>
| width="197" valign="top" | <div>'''CH-rooted'''</div>
| width="197" valign="top" | <div>'''Aromatic'''</div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-CT-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HNCO</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>HNCA</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>CBCA(CO)NH</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HBHA(CO)NH</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
| width="197" valign="top" | <div> </div>
|-
| width="590" valign="top" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| width="590" valign="top" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span>
include all the atoms belonging to the same residue; PB-fragment
includes all the atoms from one residue except the backbone amide
group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment.
</span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div> <div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span>
corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span style="display: none;" id="1259188877701S"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

=  FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:47:01Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

==== ====

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| cellspacing="0" cellpadding="0" border="0" class="FCK__ShowTableBorders"
|-
| width="197" valign="top" | <div>'''NH-rooted'''</div>
| width="197" valign="top" | <div>'''CH-rooted'''</div>
| width="197" valign="top" | <div>'''Aromatic'''</div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-CT-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HNCO</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>HNCA</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>CBCA(CO)NH</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HBHA(CO)NH</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
| width="197" valign="top" | <div> </div>
|-
| width="590" valign="top" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| width="590" valign="top" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span>
include all the atoms belonging to the same residue; PB-fragment
includes all the atoms from one residue except the backbone amide
group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment.
</span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div> <div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span>
corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span style="display: none;" id="1259188877701S"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

=  FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

Resonance Assignment/Abacus/Introduction to ABACUS

2010-01-06T18:46:45Z

RyanDoherty:

= ABACUS approach. =
<div>ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information about the "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The resonance assignment strategy of ABACUS<span> is what distinguishes it the most from conventional NMR structure determination approaches (see Fig.1.1A). </span><br></div>
==== '''Figure 1.1A''' ====

[[Image:Abacus.JPG|thumb|left|350px]]<br>

<br>

<br>

<br>

<br>

<br>

<br>'''                               '''

Flowchart of resonance assignmnent by ABACUS''. ''

<br>

<br>

<br>

<br>

<br>

==== '''<span />''' ====

==== '''<span>Some features /advantages of the ABACUS protocol:</span>''' ====

*<span><span> </span></span>It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures;
*Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;
*Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of where to focus manual intervention<font size="3">;</font>
*It can make use of partial spin-systems;
*It can efficiently identify manual errors in the input peak lists;
<div></div>
<br>

 

= NMR spectra required for ABACUS =
<div></div><div></div><div></div><div>The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted).  Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </div><div> </div><div>'''Table 1.''' '''ABACUS optimal set of experiments''' </div><div> </div>
{| cellspacing="0" cellpadding="0" border="0" class="FCK__ShowTableBorders"
|-
| width="197" valign="top" | <div>'''NH-rooted'''</div>
| width="197" valign="top" | <div>'''CH-rooted'''</div>
| width="197" valign="top" | <div>'''Aromatic'''</div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-CT-HSQC</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HNCO</div>
| width="197" valign="top" | <div><sup>13</sup>C-HSQC</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>HNCA</div>
| width="197" valign="top" | <div>H(C)CH-TOCSY</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY-aro</div>
|-
| width="197" valign="top" | <div>CBCA(CO)NH</div>
| width="197" valign="top" | <div>(H)CCH-TOCSY</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
|-
| width="197" valign="top" | <div>HBHA(CO)NH</div>
| width="197" valign="top" | <div><sup>13</sup>C-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
|-
| width="197" valign="top" | <div><sup>15</sup>N-NOESY-HSQC</div>
| width="197" valign="top" | <div> </div>
| width="197" valign="top" | <div> </div>
|-
| width="590" valign="top" colspan="3" | <div>''CCCONH-TOCSY (optional)''</div>
|-
| width="590" valign="top" colspan="3" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div> </div><div> </div><div>'''<font size="5"></font>'''</div>
= Spin-system identification strategy =
<div></div><div></div><div></div><div>The resonance assignment procedure starts from grouping resonances in spin systems. Two kind of spin-system will be considered in this manual.</div><div></div>
==== PB fragment ====
<div></div><div>PB (Peptide Bond) fragment comprise correlated resonances from the side chain of residue''i'' and the NH resonances of residue ''i+1'' (see Figure 1.1B).</div><div>
 

'''Figure 1.1B'''

[[Image:PBfragment.jpg|thumb|right|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span>
include all the atoms belonging to the same residue; PB-fragment
includes all the atoms from one residue except the backbone amide
group, plus the amide group from the next residue in the protein</span>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

 

<br>
</div><div></div>

==== ''b''PB fragment ====
<div>Uncompleted HN-rooted PB spin-systems, which include resonances of<span>   Cα, Hα, Cβ, and Hβ   atoms of residue ''i'' </span>and the NH resonances of residue ''i+1''<span>, is called ''b''PB fragment.
</span></div><div> </div><div>Spin-system identification in ABACUS approach consists of 3 main steps.</div><div> </div><div>     1. On the first step, ''b''PB fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 4.1A). </div><div> </div><div>     2. On the second step, completion of ''b''PB fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 4.1B)  </div><div> </div><div>      3. Finally, spin-system validation and correction is performed. This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </div><div> </div>
<br>

==== '''Figure 1.2<br>''' ====
<div><span>[[Image:Fmcgui Fig1.2.jpg|thumb|center|600px]]    </span></div> <div><div>For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.2). Here ''T'' corresponds to amino acid type, and ''T''=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base. Too low value of the best score S<sub>max</sub>, where <span>S<sub>max </sub></span> = max{ S(T)} ,  means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be <span>
corrected. </span></div><div> </div></div><div><br></div><div>'''<font size="5"></font>'''</div>
= Fragment assignment by FMC procedure =
<div></div><div></div><div></div><div></div><div>Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.3)</div><div> </div>
==== Figure 1.3 ====
<div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span style="display: none;" id="1259188877701S"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
==== Figure 1.4<br> ====

[[Image:Fmcgui Fig1.4.jpg|thumb|left|600px]]

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

<br>

=  FMC Graphical User Interface =
<div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>