RPF Analysis - Revision history

Jma at 17:00, 5 January 2010

2010-01-05T17:00:42Z

← Older revision		Revision as of 17:00, 5 January 2010
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	<br>		<br>

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	\| valign="top" bgcolor="#ffffff" align="center" class="twikiTableCol0 twikiFirstCol" \| NMR Data		\| valign="top" bgcolor="#ffffff" align="center" class="twikiTableCol0 twikiFirstCol" \| NMR Data
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	<br>		<br>

	~~<br>~~

	~~-- GaohuaLiu - 20 Jun 2007~~

	~~--Updated by JimAramini- 03 Nov 2009~~

	<br>		<br>

Jma at 20:26, 23 December 2009

2009-12-23T20:26:05Z

← Older revision		Revision as of 20:26, 23 December 2009
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	== '''Introduction''' ==		== '''Introduction''' ==

	RPF is a ~~modeule~~ within the AutoStructure program that uses a novel, rapid, and simple approach for calculating global NMR structure quality scores ~~(Ref.~~ 1,2). This program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores assessing how well the query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data. RPF scores quickly assess the goodness-of-fit of the query structure(s) to these experimental data, and can be used as a guide for further structure refinements. RPF also calculates discrimination power (DP) scores, which estimate the difference in F-MEASURE scores between the query structure and random coil structures, as an indictor of the correctness of the overall fold. The program is useful for quality of control protein NMR structures determined by automated or manual methods.		RPF is a module within the AutoStructure program that uses a novel, rapid, and simple approach for calculating global NMR structure quality scores [1,2]. This program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores assessing how well the query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data. RPF scores quickly assess the goodness-of-fit of the query structure(s) to these experimental data, and can be used as a guide for further structure refinements. RPF also calculates discrimination power (DP) scores, which estimate the difference in F-MEASURE scores between the query structure and random coil structures, as an indictor of the correctness of the overall fold. The program is useful for quality of control protein NMR structures determined by automated or manual methods.

	<br>		<br>
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	<br>		<br>

	{\| rules="rows" cellspacing="0" cellpadding="0" border="1" id="~~table1~~" ~~class~~="~~twikiTable~~"		{\| rules="rows" cellspacing="0" cellpadding="0" border="1" class="twikiTable" id="table1"
	\|- class="twikiTableOdd twikiTableRowdataBgSorted0 twikiTableRowdataBg0"		\|- class="twikiTableOdd twikiTableRowdataBgSorted0 twikiTableRowdataBg0"
	\| valign="top" bgcolor="#ffffff" align="center" class="twikiTableCol0 twikiFirstCol" \| NMR Data		\| valign="top" bgcolor="#ffffff" align="center" class="twikiTableCol0 twikiFirstCol" \| NMR Data
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	== '''References''' ==		== '''References''' ==

	1.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.		[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 1.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.]

	2.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.		[http://www3.interscience.wiley.com/journal/112222012/abstract 2.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.]

	<br>		<br>

Yphuang at 18:03, 18 December 2009

2009-12-18T18:03:30Z

← Older revision		Revision as of 18:03, 18 December 2009
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	{\| rules="rows" cellspacing="0" cellpadding="0" border="1" ~~class~~="~~twikiTable~~" id="~~table1~~"		{\| rules="rows" cellspacing="0" cellpadding="0" border="1" id="table1" class="twikiTable"
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	cat ali.peaks tmp > c.peaks		cat ali.peaks tmp > c.peaks
	</pre>		</pre>
	~~Janet ->~~ AutoStructure 2.2.1 or higher version does not require a single peak list for <sup>13</sup>C-resolved NOESY. No need to combine aliphatic and aromatic peak lists.		AutoStructure 2.2.1 or higher version does not require a single peak list for <sup>13</sup>C-resolved NOESY. No need to combine aliphatic and aromatic peak lists.


			<br>

	==== '''Sequence and Chemical Shift Files''' ====		==== '''Sequence and Chemical Shift Files''' ====
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	The control file is essentially the same as the one used for automated AutoStructure calculation. You may need to do the following:		The control file is essentially the same as the one used for automated AutoStructure calculation. You may need to do the following:

	*change peaklist names and paths.		*change peaklist names and paths.
	*if using separate aliphatic and aromatic peaklist - remove the aromatic peaklist entry. Janet -> No need for AutoStructure 2.2.1 or higher version.
	*comment UPL and ACO entries as they are irrelevant. Janet -> you can leave it there. <br>

	<br>		<br>

Yphuang at 15:24, 18 December 2009

2009-12-18T15:24:02Z

← Older revision		Revision as of 15:24, 18 December 2009
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	RPF is a modeule within the AutoStructure program that uses a novel, rapid, and simple approach for calculating global NMR structure quality scores (Ref. 1,2). This program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores assessing how well the query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data. RPF scores quickly assess the goodness-of-fit of the query structure(s) to these experimental data, and can be used as a guide for further structure refinements. RPF also calculates discrimination power (DP) scores, which estimate the difference in F-MEASURE scores between the query structure and random coil structures, as an indictor of the correctness of the overall fold. The program is useful for quality of control protein NMR structures determined by automated or manual methods.		RPF is a modeule within the AutoStructure program that uses a novel, rapid, and simple approach for calculating global NMR structure quality scores (Ref. 1,2). This program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores assessing how well the query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data. RPF scores quickly assess the goodness-of-fit of the query structure(s) to these experimental data, and can be used as a guide for further structure refinements. RPF also calculates discrimination power (DP) scores, which estimate the difference in F-MEASURE scores between the query structure and random coil structures, as an indictor of the correctness of the overall fold. The program is useful for quality of control protein NMR structures determined by automated or manual methods.

	<br>		<br>

	== '''Definitions''' ==		== '''Definitions''' ==
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	<br>		<br>

	{\| rules="rows" cellspacing="0" cellpadding="0" border="1" id="~~table1~~" ~~class~~="~~twikiTable~~"		{\| rules="rows" cellspacing="0" cellpadding="0" border="1" class="twikiTable" id="table1"
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	For a typical CYANA run, copy the latest peaklists from manual CYANA 2.1 structure calculation.		For a typical CYANA run, copy the latest peaklists from manual CYANA 2.1 structure calculation.

	AutoStructure 2.0 ~~and higher versions~~ require a single peaklist for <sup>13</sup>C-resolved NOESY. If you are using separate aliphatic and aromatic peaklists you need to combine them in a single peaklist.		AutoStructure 2.0 require a single peaklist for <sup>13</sup>C-resolved NOESY. If you are using separate aliphatic and aromatic peaklists you need to combine them in a single peaklist.

	For XEASY peaklists you can use the the attached [[Media:Pks.awk\|pks.awk]] script to renumber the aromatic peaks, then concatenate the result with the aliphatic peaklist:		For XEASY peaklists you can use the the attached [[Media:Pks.awk\|pks.awk]] script to renumber the aromatic peaks, then concatenate the result with the aliphatic peaklist:
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	cat ali.peaks tmp > c.peaks		cat ali.peaks tmp > c.peaks
	</pre>		</pre>
	<br>		Janet -> AutoStructure 2.2.1 or higher version does not require a single peak list for <sup>13</sup>C-resolved NOESY. No need to combine aliphatic and aromatic peak lists.



	==== '''Sequence and Chemical Shift Files''' ====		==== '''Sequence and Chemical Shift Files''' ====

	If you have modified chemical shift assignments (e.g., moved spins, added new spins) during structure refinement you should create a new chemical shift file for AutoStructure as described in [[~~Structure_calculation_with_AutoStructure~~\|Ru]][[~~Structure_calculation_with_AutoStructure~~\|nning AutoStructure]]. Otherwise, you can reuse the previous chemical shift file.		If you have modified chemical shift assignments (e.g., moved spins, added new spins) during structure refinement you should create a new chemical shift file for AutoStructure as described in [[Structure calculation with AutoStructure\|Ru]][[Structure calculation with AutoStructure\|nning AutoStructure]]. Otherwise, you can reuse the previous chemical shift file.

	The same holds for the sequence file, though it is highly unlikely that one would need to modify a protein's sequence during refinement.		The same holds for the sequence file, though it is highly unlikely that one would need to modify a protein's sequence during refinement.
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	*change peaklist names and paths.		*change peaklist names and paths.
	*if using separate aliphatic and aromatic peaklist - remove the aromatic peaklist entry.		*if using separate aliphatic and aromatic peaklist - remove the aromatic peaklist entry. Janet -> No need for AutoStructure 2.2.1 or higher version.
	*comment UPL and ACO entries as they are irrelevant.		*comment UPL and ACO entries as they are irrelevant. Janet -> you can leave it there. <br>

	<br>		<br>

Jma at 22:08, 3 December 2009

2009-12-03T22:08:25Z

← Older revision		Revision as of 22:08, 3 December 2009
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	== '''Introduction''' ==		== '''Introduction''' ==

	RPF is a modeule within the AutoStructure program that uses a novel, rapid, and simple approach for calculating global NMR structure quality scores (Ref. 1,2). This program calculates RECALL, PRECISION, and ~~FMEASURE~~ (RPF) scores assessing how well the query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data. RPF scores quickly assess the goodness-of-fit of the query structure(s) to these experimental data, and can be used as a guide for further structure refinements. RPF also calculates discrimination power (DP) scores, which estimate the difference in F-MEASURE scores between the query structure and random coil structures, as an indictor of the correctness of the overall fold. The program is useful for quality of control protein NMR structures determined by automated or manual methods.		RPF is a modeule within the AutoStructure program that uses a novel, rapid, and simple approach for calculating global NMR structure quality scores (Ref. 1,2). This program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores assessing how well the query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data. RPF scores quickly assess the goodness-of-fit of the query structure(s) to these experimental data, and can be used as a guide for further structure refinements. RPF also calculates discrimination power (DP) scores, which estimate the difference in F-MEASURE scores between the query structure and random coil structures, as an indictor of the correctness of the overall fold. The program is useful for quality of control protein NMR structures determined by automated or manual methods.

	<br>		<br>

	== '''Definitions''' ==		== '''Definitions''' ==

Jma at 20:24, 3 December 2009

2009-12-03T20:24:36Z

← Older revision		Revision as of 20:24, 3 December 2009
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	== '''Introduction''' ==		== '''Introduction''' ==

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	<br>		<br>

	{\| rules="rows" cellspacing="0" cellpadding="0" border="1" ~~class~~="~~twikiTable~~" id="~~table1~~"		{\| rules="rows" cellspacing="0" cellpadding="0" border="1" id="table1" class="twikiTable"
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	==== '''Peaklists''' ====		==== '''Peaklists''' ====

	Like AutoStructure, peak lists in either [[Sparky~~\|Sparky]]~~ or Xeasy formats can be used with the RPF program.		Like AutoStructure, peak lists in either Sparky or Xeasy formats can be used with the RPF program.

	For a typical CYANA run, copy the latest peaklists from manual ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~CYANA ~~CYANA]~~ 2.1 structure calculation.		For a typical CYANA run, copy the latest peaklists from manual CYANA 2.1 structure calculation.

	~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoStructure ~~AutoStructure]~~ 2.0 and higher versions require a single peaklist for <sup>13</sup>C-resolved NOESY. If you are using separate aliphatic and aromatic peaklists you need to combine them in a single peaklist.		AutoStructure 2.0 and higher versions require a single peaklist for <sup>13</sup>C-resolved NOESY. If you are using separate aliphatic and aromatic peaklists you need to combine them in a single peaklist.

	For ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~XEASY ~~XEASY]~~ peaklists you can use the the attached [[Media:Pks.awk\|pks.awk]] script to renumber the aromatic peaks, then concatenate the result with the aliphatic peaklist:		For XEASY peaklists you can use the the attached [[Media:Pks.awk\|pks.awk]] script to renumber the aromatic peaks, then concatenate the result with the aliphatic peaklist:

	<br>		<br>
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	==== '''Sequence and Chemical Shift Files''' ====		==== '''Sequence and Chemical Shift Files''' ====

	If you have modified chemical shift assignments (e.g., moved spins, added new spins) during structure refinement you should create a new chemical shift file for ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoStructure ~~AutoStructure]~~ as described in [~~http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/AutoStructureRun Running~~ AutoStructure]. Otherwise, you can reuse the previous chemical shift file.		If you have modified chemical shift assignments (e.g., moved spins, added new spins) during structure refinement you should create a new chemical shift file for AutoStructure as described in [[Structure_calculation_with_AutoStructure\|Ru]][[Structure_calculation_with_AutoStructure\|nning AutoStructure]]. Otherwise, you can reuse the previous chemical shift file.

	The same holds for the sequence file, though it is highly unlikely that one would need to modify a protein's sequence during refinement.		The same holds for the sequence file, though it is highly unlikely that one would need to modify a protein's sequence during refinement.
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	==== '''Control File''' ====		==== '''Control File''' ====

	The control file is essentially the same as the one used for automated ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoStructure ~~AutoStructure]~~ calculation. You may need to do the following:		The control file is essentially the same as the one used for automated AutoStructure calculation. You may need to do the following:

	*change peaklist names and paths.		*change peaklist names and paths.
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	*<code>write coor pdb XXXX_ref.pdb</code>		*<code>write coor pdb XXXX_ref.pdb</code>

	Here we assume that the output of ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~CNS ~~CNS]~~ is =All_KKK_cns.pdb.		Here we assume that the output of CNS is =All_KKK_cns.pdb.

	~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoStructure ~~AutoStructure]~~ is sensitive to the atom name nomenclature of the PDB input file. In the output directory (e.g. <code>calcQ</code>) check the contents of the <code>XXXX_NA.note</code> file to see if the PDB file has been read correctly.		AutoStructure is sensitive to the atom name nomenclature of the PDB input file. In the output directory (e.g. <code>calcQ</code>) check the contents of the <code>XXXX_NA.note</code> file to see if the PDB file has been read correctly.

	<br>		<br>

	== '''Using ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoStructure ~~AutoStructure]~~ in shell mode''' ==		== '''Using AutoStructure in shell mode''' ==

	To start RPF analysis type<br>		To start RPF analysis type<br>
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	<br>		<br>

	== '''Using ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoStructure ~~AutoStructure]~~ in GUI mode''' ==		== '''Using AutoStructure in GUI mode''' ==

	~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoStructure ~~AutoStructure]~~ version 2.1.1 and higher has a GUI for RPF analysis providing additional features. However, older Linux systems may not have the proper graphics libraries to support it.		AutoStructure version 2.1.1 and higher has a GUI for RPF analysis providing additional features. However, older Linux systems may not have the proper graphics libraries to support it.

	The RPF interface (From ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoStructure ~~AutoStructure]~~ interface) provides a useful interface for the user to calculate RPF scores. Structures determined by manual or automated analysis, homology modelling, or X-ray crystallography can be used for RPF scores calculations.		The RPF interface (From AutoStructure interface) provides a useful interface for the user to calculate RPF scores. Structures determined by manual or automated analysis, homology modelling, or X-ray crystallography can be used for RPF scores calculations.

	To run: type <code>asgui</code>		To run: type <code>asgui</code>
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	For one pdb file: select from menu: <code>AutoQF(RPF)</code> -> <code>Calc</code> -> <code>One</code>		For one pdb file: select from menu: <code>AutoQF(RPF)</code> -> <code>Calc</code> -> <code>One</code>

	For ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/AutoStructure~~ AutoStructure] Output directory: select from menu: <code>AutoQF(RPF)</code> -> <code>Calc</code> - > <code>For ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/AutoStructure~~ AutoStructure] Output Dir</code>		For AutoStructure Output directory: select from menu: <code>AutoQF(RPF)</code> -> <code>Calc</code> - > <code>For AutoStructure Output Dir</code>

	Open Output: select from menu: <code>AutoQF(RPF)</code> -> <code>Open RPF directory</code>		Open Output: select from menu: <code>AutoQF(RPF)</code> -> <code>Open RPF directory</code>
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	<br>		<br>

	=== '''Quality control for iterative cycle analysis using the output of ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoStructure ~~AutoStructure]~~''' ===		=== '''Quality control for iterative cycle analysis using the output of AutoStructure''' ===

	RPF scores can be used as a quality control in iterative cycle analysis of protein structure determination in NMR. The RPF interface (shown in the figure below) displays the results of the iterative cycle analysis of NMR structure determination as a plot of the RPF and DP scores. The significant increase in the DP score from cycle 1 to cycle 10 demonstrates the improved accuracy of the final structure when compared to the initial and intermediate cycles. By the final cycle the F-measure is > 0.9 and the DP score is > 0.7 which correlates to structures having accuracies of < ~ 2 Å rmsd. During the iterative refinement process, as long as the structure does not have many bad proton-proton packing interactions, the Precision rate should be high and stay relatively constant. The below figure shows that Precision rates decrease slightly during the iterative process. This is due to the increased compactness of the structure over the course of the refinement, when additional weak NOE cross peaks predicted are missing from the input NOE peak lists (False Positives). The small decrease in precision over the course of refinement is diagnostic of the quality and completeness of the input NMR data.  In AutoStructure 2.4.0, RPF scores for individual models in the structural ensemble are also reported.		RPF scores can be used as a quality control in iterative cycle analysis of protein structure determination in NMR. The RPF interface (shown in the figure below) displays the results of the iterative cycle analysis of NMR structure determination as a plot of the RPF and DP scores. The significant increase in the DP score from cycle 1 to cycle 10 demonstrates the improved accuracy of the final structure when compared to the initial and intermediate cycles. By the final cycle the F-measure is > 0.9 and the DP score is > 0.7 which correlates to structures having accuracies of < ~ 2 Å rmsd. During the iterative refinement process, as long as the structure does not have many bad proton-proton packing interactions, the Precision rate should be high and stay relatively constant. The below figure shows that Precision rates decrease slightly during the iterative process. This is due to the increased compactness of the structure over the course of the refinement, when additional weak NOE cross peaks predicted are missing from the input NOE peak lists (False Positives). The small decrease in precision over the course of refinement is diagnostic of the quality and completeness of the input NMR data.  In AutoStructure 2.4.0, RPF scores for individual models in the structural ensemble are also reported.
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	<br>		<br>

	-- ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/Main/~~GaohuaLiu ~~GaohuaLiu]~~ - 20 Jun 2007		-- GaohuaLiu - 20 Jun 2007

	--Updated by JimAramini- 03 Nov 2009		--Updated by JimAramini- 03 Nov 2009

Jma at 17:51, 7 November 2009

2009-11-07T17:51:45Z

← Older revision		Revision as of 17:51, 7 November 2009
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	<br>		<br>

	== References ==		== '''References''' ==

	1.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.		1.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.

Jma at 21:47, 5 November 2009

2009-11-05T21:47:41Z

← Older revision		Revision as of 21:47, 5 November 2009
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	~~= '''RPF Scores for Structure Validation'''<br> =~~

	== '''Introduction''' ==		== '''Introduction''' ==
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	<br>		<br>

	{\| rules="rows" cellspacing="0" cellpadding="0" border="1" id="~~table1~~" ~~class~~="~~twikiTable~~"		{\| rules="rows" cellspacing="0" cellpadding="0" border="1" class="twikiTable" id="table1"
	\|- class="twikiTableOdd twikiTableRowdataBgSorted0 twikiTableRowdataBg0"		\|- class="twikiTableOdd twikiTableRowdataBgSorted0 twikiTableRowdataBg0"
	\| valign="top" bgcolor="#ffffff" align="center" class="twikiTableCol0 twikiFirstCol" \| NMR Data		\| valign="top" bgcolor="#ffffff" align="center" class="twikiTableCol0 twikiFirstCol" \| NMR Data
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	[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/AutoStructure AutoStructure] 2.0 and higher versions require a single peaklist for <sup>13</sup>C-resolved NOESY. If you are using separate aliphatic and aromatic peaklists you need to combine them in a single peaklist.		[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/AutoStructure AutoStructure] 2.0 and higher versions require a single peaklist for <sup>13</sup>C-resolved NOESY. If you are using separate aliphatic and aromatic peaklists you need to combine them in a single peaklist.

	For [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY] peaklists you can use the the attached [[~~media~~:~~pks~~.awk\|pks.awk]] script to renumber the aromatic peaks, then concatenate the result with the aliphatic peaklist:		For [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY] peaklists you can use the the attached [[Media:Pks.awk\|pks.awk]] script to renumber the aromatic peaks, then concatenate the result with the aliphatic peaklist:

	<br>		<br>
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	cat ali.peaks tmp > c.peaks		cat ali.peaks tmp > c.peaks
	</pre>		</pre>
	<br>		<br>

	==== '''Sequence and Chemical Shift Files''' ====		==== '''Sequence and Chemical Shift Files''' ====
Line 172:		Line 171:
	== References ==		== References ==

	1.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.		1.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.

	2.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.


			2.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.

			<br>

			<br>

	-- [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/Main/GaohuaLiu GaohuaLiu] - 20 Jun 2007		-- [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/Main/GaohuaLiu GaohuaLiu] - 20 Jun 2007
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	[[Media:Pks.awk\|pks.awk]] : awk script to renumber peaks from a peaklist		[[Media:Pks.awk\|pks.awk]] : awk script to renumber peaks from a peaklist

Jma: moved AutoStructureRPFScores to RPF Analysis

2009-11-05T21:45:36Z

moved AutoStructureRPFScores to RPF Analysis

← Older revision	Revision as of 21:45, 5 November 2009
(No difference)

Jma at 22:21, 3 November 2009

2009-11-03T22:21:42Z

← Older revision		Revision as of 22:21, 3 November 2009
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	== References ==		== References ==

			1.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.

			2.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.





	-- [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/Main/GaohuaLiu GaohuaLiu] - 20 Jun 2007		-- [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/Main/GaohuaLiu GaohuaLiu] - 20 Jun 2007
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	[[~~media~~:~~pks~~.awk\|pks.awk]] : awk script to renumber peaks from a peaklist		[[Media:Pks.awk\|pks.awk]] : awk script to renumber peaks from a peaklist