PSVS - Revision history

Krishna: /* Introduction */

2020-04-29T18:33:15Z

Introduction

← Older revision		Revision as of 18:33, 29 April 2020
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	[~~http~~://~~www-nmr~~.~~cabm~~.~~rutgers~~.edu/PSVS/ PSVS] (Protein Structure Validation Server) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses [1]. PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>		[https://montelionelab.chem.rpi.edu/PSVS/ PSVS] (Protein Structure Validation Server) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses [1]. PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>

	<br>		<br>

	== '''Running the PSVS server''' ==		== '''Running the PSVS server''' ==

Krishna: /* Running the PSVS server */

2020-04-29T18:27:07Z

Running the PSVS server

← Older revision		Revision as of 18:27, 29 April 2020
Line 7:		Line 7:
	== '''Running the PSVS server''' ==		== '''Running the PSVS server''' ==

	Once the structure is available, go to the [~~http~~://~~www-nmr~~.~~cabm~~.~~rutgers~~.edu/PSVS/ PSVS server] and upload the input files as described in that page (Figure 1).<br>		Once the structure is available, go to the [https://montelionelab.chem.rpi.edu/PSVS/ PSVS server] and upload the input files as described in that page (Figure 1).<br>

	*PDB coordinates: atom names can be in PDB format, DYANA/CYANA or CNS/XPLOR format		*PDB coordinates: atom names can be in PDB format, DYANA/CYANA or CNS/XPLOR format
Line 20:		Line 20:
	[[Image:PSVS1.4 titlepage.png\|800px]]		[[Image:PSVS1.4 titlepage.png\|800px]]

	<br>		<br>

	== '''PSVS Output''' ==		== '''PSVS Output''' ==

Jma at 16:57, 7 January 2010

2010-01-07T16:57:08Z

← Older revision		Revision as of 16:57, 7 January 2010
Line 37:		Line 37:
	<br>		<br>

	===== Figure 2:  PSVS 1.4 output page ~~(partial)~~ =====		===== Figure 2:  PSVS 1.4 output page =====

	[[Image:PSVS1.~~4_outputpage_new~~.png\|1000px]]<br>		[[Image:PSVS1.4_outputpage_new2.png\|1000px]]<br>

	<br>		<br>

Jma at 16:41, 7 January 2010

2010-01-07T16:41:14Z

← Older revision		Revision as of 16:41, 7 January 2010
Line 16:		Line 16:
	<br>		<br>

	===== Figure 1:  PSVS input page =====		===== Figure 1:  PSVS 1.4 input page =====

	[[Image:PSVS1.4 titlepage.png\|800px]]		[[Image:PSVS1.4 titlepage.png\|800px]]
Line 37:		Line 37:
	<br>		<br>

	===== Figure 2:  PSVS~~ ~~output page =====		===== Figure 2:  PSVS 1.4 output page (partial) =====

	[[Image:PSVS1.~~4 outputpage~~.png\|1000px]]		[[Image:PSVS1.4_outputpage_new.png\|1000px]]<br>

	<br>		<br>

Jma at 17:01, 5 January 2010

2010-01-05T17:01:15Z

← Older revision		Revision as of 17:01, 5 January 2010
Line 45:		Line 45:
	== '''References''' ==		== '''References''' ==

	[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795.]		[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795.]

	~~<br> -- Main.GaohuaLiu - 05 Feb 2007~~

	~~-- Updated by JimAramini - 31 Oct 2009~~

Jma at 20:29, 23 December 2009

2009-12-23T20:29:04Z

← Older revision		Revision as of 20:29, 23 December 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	[http://www-nmr.cabm.rutgers.edu/PSVS/ PSVS] (Protein Structure Validation Server) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses ~~(Ref.~~ 1). PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>		[http://www-nmr.cabm.rutgers.edu/PSVS/ PSVS] (Protein Structure Validation Server) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses [1]. PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>

	<br>		<br>
Line 45:		Line 45:
	== '''References''' ==		== '''References''' ==

	1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795.		[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795.]

	<br> -- Main.GaohuaLiu - 05 Feb 2007		<br> -- Main.GaohuaLiu - 05 Feb 2007

	-- Updated by JimAramini - 31 Oct 2009		-- Updated by JimAramini - 31 Oct 2009

Jma at 22:45, 11 November 2009

2009-11-11T22:45:43Z

← Older revision		Revision as of 22:45, 11 November 2009
Line 18:		Line 18:
	===== Figure 1:  PSVS input page =====		===== Figure 1:  PSVS input page =====

	[[Image:PSVS1.4 titlepage.png\|~~800x600px~~]]		[[Image:PSVS1.4 titlepage.png\|800px]]

	<br>		<br>
Line 39:		Line 39:
	===== Figure 2:  PSVS output page =====		===== Figure 2:  PSVS output page =====

	[[Image:PSVS1.4 outputpage.png\|~~1000x600px~~]]		[[Image:PSVS1.4 outputpage.png\|1000px]]

	<br>		<br>

Jma at 21:53, 5 November 2009

2009-11-05T21:53:33Z

← Older revision		Revision as of 21:53, 5 November 2009
Line 1:		Line 1:
	~~='''Protein Structure Validation Suite (PSVS)'''=~~
	== '''Introduction''' ==		== '''Introduction''' ==

	[http://www-nmr.cabm.rutgers.edu/PSVS/ PSVS] (~~protein structure validation server~~) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses (Ref. 1). PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>		[http://www-nmr.cabm.rutgers.edu/PSVS/ PSVS] (Protein Structure Validation Server) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses (Ref. 1). PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>

	<br>		<br>

Jma at 18:35, 3 November 2009

2009-11-03T18:35:27Z

← Older revision		Revision as of 18:35, 3 November 2009
Line 1:		Line 1:
			='''Protein Structure Validation Suite (PSVS)'''=
	== '''Introduction''' ==		== '''Introduction''' ==

	[http://www-nmr.cabm.rutgers.edu/PSVS/ PSVS] (protein structure validation server) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses (Ref. 1). PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>		[http://www-nmr.cabm.rutgers.edu/PSVS/ PSVS] (protein structure validation server) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses (Ref. 1). PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>

	<br>		<br>

	== '''Running the PSVS server''' ==		== '''Running the PSVS server''' ==
Line 35:		Line 36:
	**RPF Scores (optional). A good structure should have R > 90%, P > 90%, F> 90% and DP > 70%.		**RPF Scores (optional). A good structure should have R > 90%, P > 90%, F> 90% and DP > 70%.

			<br>

			===== Figure 2:  PSVS output page =====

	~~===== Figure 2~~:~~  PSVS output page =====~~		[[Image:PSVS1.4 outputpage.png\|1000x600px]]

	~~[[Image:PSVS1.4_outputpage.png\|1000x600px]]~~		<br>

	<br>

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

Jma at 22:12, 31 October 2009

2009-10-31T22:12:47Z

← Older revision		Revision as of 22:12, 31 October 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	[http://www-nmr.cabm.rutgers.edu/PSVS/ PSVS] (protein structure validation server) systematically evaluates the quality of protein structures~~. PSVS~~ reports a set of quality scores and constraint ~~analyzes~~. PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>		[http://www-nmr.cabm.rutgers.edu/PSVS/ PSVS] (protein structure validation server) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses (Ref. 1). PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.  <br>

	<br>		<br>

	== '''Running the PSVS server''' ==		== '''Running the PSVS server''' ==