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<big>'''Welcome to the NESG Wiki!'''</big><br>  
<big>'''Welcome to the NESG Wiki!'''</big><br>  


For a more linear view of the contents see [[Wiki Tree Layout]]
The NESG Wiki is a medium for sharing experimental protocols as well as training an educational materials in the fields of structural biology, structural genomics and biomolecular NMR.


== Protein sample production  ==
Please check out [[NESG NMR wiki workshop at the 2010 Keystone meeting|NESG NMR wiki workshop presentations at the 2010 Keystone meeting]]


{| cellspacing="1"
== Protein Sample Production  ==
 
{| cellspacing="1" class="FCK__ShowTableBorders"
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**[[Construct optimization]]  
**[[Construct optimization]]  
**[[Buffer optimization]]  
**[[Buffer optimization]]  
**[[Cofactor optimization]]  
**[[Cofactor optimization]]
|
 
*[[SDS page gel]]  
|  
*[[Protein concentration|Protein concentration measurements]]  
*Protein Sample Analysis
*[[Oligomerization Status|Assessment of Oligomerization Status]]  
**[[SDS page gel]]  
**[[Gel filtration and light scattering|gel-filtration and light scattering]]  
**[[Protein concentration|Protein concentration measurements]]  
**[[NMR determined Rotational correlation time]]  
**[[Oligomerization Status|Assessment of Oligomerization State]]  
*[[MassSpectrometry|Mass spectrum]]  
***[[Gel filtration and light scattering|gel-filtration and light scattering]]  
*NMR screening
***[[NMR determined Rotational correlation time]]  
**[[1D screening|<sup>1</sup>H 1D screening]]  
**[[MassSpectrometry|Mass spectrum]]  
**[[Nhsqc screen|Initial [<sup>15</sup>N,<sup>1</sup>H] HSQC]]<br>
**[[NMR screening]]
 
 
 
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|}


== NMR Data Acquisition  ==
== NMR Data Acquisition  ==


{| cellspacing="1"
{| class="FCK__ShowTableBorders" cellspacing="1"
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*Routine operation  
*Routine operation  
**[[NMR sample tubes]]
**[[NMR Sample Preparation]]  
**[[NMR Sample Preparation]]  
**[[Inserting NMR Sample]]  
**[[Inserting NMR Sample]]  
**Tuning and matching  
**[[Tuning and matching]]
**[[Deuterium Lock]]  
**[[Deuterium Lock]]  
**[[Shimming]]  
**[[Shimming]]  
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*Advanced operation  
*Advanced operation  
**[[Deuterium pulse width calibration and decoupling]]
**[[Deuterium pulse width calibration and decoupling]]
|
 
|  
*NMR data acquisition for protein structure determination  
*NMR data acquisition for protein structure determination  
**[[Common NMR experiment sets]]  
**[[Common NMR experiment sets]]  
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**[[Simultaneous 13C,15N-resolved NOESY]]  
**[[Simultaneous 13C,15N-resolved NOESY]]  
**[[2D (13C, 1H) HSQC for fractionally 13C-labeled samples|2D [13C, 1H]-HSQC for fractionally 13C-labeled samples]]  
**[[2D (13C, 1H) HSQC for fractionally 13C-labeled samples|2D [13C, 1H]-HSQC for fractionally 13C-labeled samples]]  
**[[Long-range 15N-1H correlation experiments for histidine rings]]
**[[Long-range 15N-1H correlation experiments for histidine rings]]  
*Non-uniform sampling (NUS)
*[[Setting up non-uniformly sampled spectra|Non-uniform sampling (NUS) ]]
**[[Setting up non-uniformly sampled spectra/NUS guide for Varian|NUS - Varian]]  
**[[Setting up non-uniformly sampled spectra/NUS guide for Varian|NUS - Varian]]  
**[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|NUS - Bruker]]  
**[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|NUS - Bruker]]
|
 
*Maintenance (VARIAN)
|  
*Maintenance (VARIAN)  
**[[Installing and updating BioPack]]  
**[[Installing and updating BioPack]]  
**[[Full probefile calibration]]  
**[[Full probefile calibration]]  
**[[Rebooting spectrometer console]]  
**[[Rebooting spectrometer console]]  
**[[Conditioning procedure for cryogenic probes]]   
**[[Conditioning procedure for cryogenic probes]]
 
|}
 
== NMR Data Processing ==
 
{| class="FCK__ShowTableBorders" cellspacing="1"
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NMRPipe
 
*[[Brief description of philosophy, commands, and functions of NMRPipe|Brief description of philosophy, commands, and functions]]
*[[Routine 2D Experiment|2D experiments]]
*[[Routine Processing Procedure for 3D 15N and 13C-edited Experiments|3D <sup>15</sup>N and <sup>13</sup>C-edited experiments]]
*[[HSQCTROSY RDC Measurement|2D ]]<sup>[[HSQCTROSY RDC Measurement|15]]</sup>[[HSQCTROSY RDC Measurement|N HSQC-TROSY experiment for RDC measurement]]
*[[Jmodulation Experiment RDC|2D J-modulation experiment for RDC measurement]]
*[[Alignment Media Preparation|Alignment Media Preparation for RDC measurement]]
 
|
Other
 
*[[Processing NMR spectra with PROSA|PROSA]]
*[[Bruker Data Processing|TOPSPIN]]
*[[AGNuS/AutoProc|AUTOPROC]]
*[[Processing non-uniformly sampled spectra with Multidimensional Decomposition|Processing NUS spectra with MDD]]
*[[Spectra Format Conversion from NMRPipe Data|NMRPipe processed data conversion to Sparky, CARA, XEASY, and NMRViewJ]]
 
|}
|}


== Resonance Assignment  ==
== NMR Resonance Assignment  ==
{| cellspacing="1"
 
*[[Resonance Assignment/Principles and concepts|Principles and concepts]]
 
{| class="FCK__ShowTableBorders" cellspacing="1"
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*[[Resonance Assignment/Principles and concepts|Principles and concepts]]
*Semi-automated protocols  
*Semi-automated protocols  
**[[CARA]]
**[[Resonance Assignment/CARA|CARA]]  
**[[Sparky]]  
**[[Sparky]]  
**[[XEASY]]
**[[Resonance Assignment/XEASY|XEASY]]
|
 
|  
*Automated resonance assignment  
*Automated resonance assignment  
**[[AutoAssign|AutoAssign]]  
**[[AutoAssign|AutoAssign]]  
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**[[Abacus|ABACUS]]  
**[[Abacus|ABACUS]]  
**[[The PINE Server|PINE server]]
**[[The PINE Server|PINE server]]
|
 
|  
*Validation and deposition  
*Validation and deposition  
**[[AVS|Assignment validation suite (AVS)]]  
**[[AVS|Assignment validation suite (AVS)]]  
**[[LACS|Linear analysis of chemical shift (LACS)]]  
**[[LACS|Linear analysis of chemical shift (LACS)]]  
**[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]
**[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]
|}
|}


{|
== Structure Calculation and Validation  ==
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[[Structure Calculation and Validation|Principles and concepts]]


#[[Resonance Assignment/Principles and concepts|Principles and concepts]]
{| class="FCK__ShowTableBorders" cellspacing="1"
#[[Resonance Assignment/Practical aspects|Practical aspects]]
|- valign="top"
##Semi-automated protocols
|
###[[CARA]]
*Structure calculation
####[[Spin System Identification with CARA|Spin System Identification in 2D 15N-HSQC and 3D HNNCO]]
**[[CYANA Structure Determination Program|CYANA]]  
####[[Backbone Assignment with CARA|Backbone Resonance Assignment]]  
**[[AutoStructure Structure Determination Program|AutoStructure]]  
####[[HA and HB Assignment with CARA|Assignment of HA and HB Resonances with (4,3)D GFT HABCAB(CO)NHN]]  
**[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]]  
####Side Chain Assignment
**[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]]  
#####[[Aliphatic Side Chain Assignment with CARA|Aliphatic side-chain assignment]]
**[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]]  
#####[[Aromatic Side Chain Assignment with CARA|Aromatic side-chain assignment]]  
**[[Consensus Approaches|"Consensus" approaches]]  
#####[[Amide Side Chain Assignment with CARA|Amide side-chain assignment]]
**[[Refinement Strategies|Refinement Strategies]]
###[[Sparky]]
###[[XEASY]]
####[[XEASY Spin system identification|Spin system identification]]
####Backbone resonance assignment'''<br>'''
#####GFT-based spectra
######[[HNCACAB/CABCA(CO)NH]]  
#####Conventional spectra
######[[HNCACB/CBCA(CO)NH]]
######HNCA/HN(CO)CA
######HNCO/HN(CA)CO
######NOESY/TOCSY
####[[XEASY Side Chain Assignment|Side chain resonance assignment]]
#####Aliphatic
######GFT NMR spectra
#######[[HA and HB Assignment with GFT in XEASY|(4,3)D GFT HABCAB(CO)NHN]]
#######[[Side chain assignment with aliphatic (4,3)D HCCH-COSY in XEASY|(4,3)D GFT HCCH]]
######Conventional spectra
#######HAHB(CO)NH
#######HCCH-COSY
#######HCCH-TOCSY
#######[[Side chain assignment with CN-NOESY in XEASY|Simultaneous NOESY]]
#######(H)CC-TOCSY-(CO)NH
#######H(CC-TOCSY-CO)NH
#####[[Aromatic side chain assignment with Aro-HCCH-COSY in XEASY|Aromatic]]
######GFT-based spectra
######Conventional spectra
#####Other
######Trp e1 NH and d1 CH
######[[Met methyl assignment with NOESY|Met e CH3 ]]
######[[Amide Side Chain assignment with NOESY|Asn d2 and Gln e2 NH2]]
#####NOESY peak integration
##Automated protocols
###[[AutoAssign|AutoAssign]]
###[[AutoAssign WebServer|AutoAssign server]]
###[[Abacus|ABACUS]]
###[[The PINE Server|PINE server]]
##Validation of resonance assignment
###[[AVS|Assignment validation suite (AVS)]]  
###[[LACS|Linear analysis of chemical shift (LACS)]]  
##[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]


| style="border: 1px solid rgb(170, 170, 170); padding: 1em; background: rgb(255, 239, 240) none repeat scroll 0% 0%; width: 33%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;" |  
|  
=== Structure Calculation and Validation  ===
*Special topics
**[[Protein-Ligand Complexes|Protein-Ligand complexes]]
**[[Working With Metal Ions|Metal ions]]
**[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]
**[[REDCAT|REDCAT]] and [[REDCRAFT|REDCRAFT]]
**[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]
**[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]


#[[Structure Calculation and Validation|Principles and concepts]]
|  
#Practical aspects
*Structure Refinement  
##Structure calculation
**[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]]  
###CYANA
**[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]]  
####[[CYANA|Getting started]]
**[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]]<br>
####[[FOUND|FOUND]]
####[[TALOS|TALOS]]
####[[GLOMSA|GLOMSA]]
####[[NOE Calibration Using CYANA|NOE calibration]]
####[[Manual Structure Calculation Using CYANA|Manual structure calculation]]
####[[Automated NOESY Assignment Using CYANA|Automated NOESY assignment and structure calculation]]
####[[Structure Calculation With RDC's Using CYANA|Structure calculation with residual dipolar couplings]] (link to REDCAT/PALES,FINDTENSOR, .rdc file, adding ORI to PDB file)
####[[Homodimer Structure Calculation Using CYANA|Homodimer structure calculations]][[Homodimer Structure Calculation Using CYANA|<br>]]
###AutoStructure
####[[AutoStructure/RPF Theory|Theory]]
####[[AutoStructure|Getting started]]
####[[CYANA Structure Calculations Using AutoStructure|CYANA run]]
####[[XPLOR Structure Calculations Using AutoStructure|XPLOR run]]
####[[Analyzing AutoStructure Output Directories|Analyzing the output]]
####[[RPF Analysis|RPF/DP scores]]
####[[Structure Calculation Using AS-DP|Structure calculation using AS-DP]]
###"Consensus"&nbsp;Approaches
####[[Overview of Consensus Runs|Overview of Consensus runs]]
####[[Finding Consensus NOE Assignments|Finding Consensus NOE assignments]]
####[[Validation of Consensus Run|Validation of Consensus runs]]
###[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]]
###[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]]
###[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]]
###[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]<br>
###Special topics
####[[Protein-Ligand Complexes|Protein-Ligand complexes]]
####[[Working With Metal Ions|Metal ions]]
####[[Working With Dimers|Dimers]]
####[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]
####[[REDCAT|REDCAT]]&nbsp;and [[REDCRAFT|REDCRAFT]]
####[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]
##Structure Refinement
###[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]]  
###[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]]  
###[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]]  
##Validation and deposition
###[[PdbStat|PdbStat]]
###[[PSVS|PSVS]]
###[[RPF Analysis|RPF analysis]]
###[[MolProbity Server|MolProbity server]]
###[[PDB and BMRB Deposition|PDB and BMRB deposition]]
###[[ADIT-NMR|ADIT-NMR]]
###[[HarvestDB|HarvestDB]]
###[[SPINS|SPINS]]


|}
|  
*Validation and deposition
**[[PdbStat|PdbStat]]
**[[PSVS|PSVS]]
**[[RPF Analysis|RPF analysis]]
**[[MolProbity Server|MolProbity server]]
**[[RDCvis & KiNG|RDCvis]]
**[[PDB and BMRB Deposition|PDB and BMRB deposition]]
**[[ADIT-NMR|ADIT-NMR]]
**[[HarvestDB|HarvestDB]]
**[[SPINS|SPINS]]


<br> <br>
|}
 
== Getting started  ==
 
*[http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
*[http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
*[https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Latest revision as of 02:29, 29 November 2022


Welcome to the NESG Wiki!

The NESG Wiki is a medium for sharing experimental protocols as well as training an educational materials in the fields of structural biology, structural genomics and biomolecular NMR.

Please check out NESG NMR wiki workshop presentations at the 2010 Keystone meeting

Protein Sample Production


NMR Data Acquisition

NMR Data Processing

NMRPipe

Other

NMR Resonance Assignment

Structure Calculation and Validation

Principles and concepts

Retrieved from "https://nesgwiki.chem.buffalo.edu/index.php?title=Main_Page&oldid=4368"