MolProbity Server - Revision history

Jma at 17:00, 5 January 2010

2010-01-05T17:00:03Z

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

	~~--JimAramini - 02 Nov 2009~~<br><br>		<br><br>

Jma at 20:16, 23 December 2009

2009-12-23T20:16:56Z

← Older revision		Revision as of 20:16, 23 December 2009
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	== '''Introduction''' ==		== '''Introduction''' ==

	The MolProbity server, developed by the Richardson group ~~(Ref.~~ 1,2), is a site for the evaluation of single X-ray structures and NMR structure ensembles.  The server performs a number of validations including all-residue Ramachandran analysis, rotamer analysis, and all-atom clash analysis.  Like the PSVS server, the MolProbity server is a valuable structure validation tool in the final stages of structure refinement.  Structures and various metrics are visualized in the KiNG tool, and all analyses and “kinemages” can be downloaded.   The server can be accessed at: [http://molprobity.biochem.duke.edu/ http://molprobity.biochem.duke.edu/].		The MolProbity server, developed by the Richardson group [1,2], is a site for the evaluation of single X-ray structures and NMR structure ensembles.  The server performs a number of validations including all-residue Ramachandran analysis, rotamer analysis, and all-atom clash analysis.  Like the PSVS server, the MolProbity server is a valuable structure validation tool in the final stages of structure refinement.  Structures and various metrics are visualized in the KiNG tool, and all analyses and “kinemages” can be downloaded.   The server can be accessed at: [http://molprobity.biochem.duke.edu/ http://molprobity.biochem.duke.edu/].

	== '''Using MolProbity server''' ==		== '''Using MolProbity server''' ==
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	== '''References''' ==		== '''References''' ==

	1.    Davis, I.W., Leaver-Fay, A., Chen, V.B., Block, J.N., Kapral, G.J., Wang, X., Murray, L.W., Arendall III, W.B., Snoeyink, J., Richardson, J.S. and Richardson, D.C. (2007) MolProbity:  all-atom contacts and structure validation for proteins and nucleic acids. ''Nucleic Acids Res. 35'', W375-W383.<br>2.    Lovell, S.C., Davis, I.W., Arendall III, W.B., de Bakker, P.I.W., Word, J.M., Prisant, M.G., Richardson, J.S. and Richardson, D.C. (2003) Structure validation by Cα geometry: φ, ψ, and Cβ deviation.  ''Proteins 50'', 437-450.		[http://www.ncbi.nlm.nih.gov/pubmed/17452350?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2 1.    Davis, I.W., Leaver-Fay, A., Chen, V.B., Block, J.N., Kapral, G.J., Wang, X., Murray, L.W., Arendall III, W.B., Snoeyink, J., Richardson, J.S. and Richardson, D.C. (2007) MolProbity:  all-atom contacts and structure validation for proteins and nucleic acids. ''Nucleic Acids Res. 35'', W375-W383.]<br>[http://www3.interscience.wiley.com/journal/102523245/abstract?CRETRY=1&SRETRY=0 2.    Lovell, S.C., Davis, I.W., Arendall III, W.B., de Bakker, P.I.W., Word, J.M., Prisant, M.G., Richardson, J.S. and Richardson, D.C. (2003) Structure validation by Cα geometry: φ, ψ, and Cβ deviation.  ''Proteins 50'', 437-450.]

	<br>		<br>

	--JimAramini - 02 Nov 2009<br><br>		--JimAramini - 02 Nov 2009<br><br>

Jma: moved MolProbity server to MolProbity Server

2009-11-05T21:51:45Z

moved MolProbity server to MolProbity Server

← Older revision	Revision as of 21:51, 5 November 2009
(No difference)

Jma at 21:44, 5 November 2009

2009-11-05T21:44:26Z

← Older revision		Revision as of 21:44, 5 November 2009
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	~~= '''MolProbity Server''' =~~

	== '''Introduction''' ==		== '''Introduction''' ==

Jma at 18:34, 3 November 2009

2009-11-03T18:34:17Z

← Older revision		Revision as of 18:34, 3 November 2009
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	='''MolProbity Server''=		= '''MolProbity Server''' =

	== '''Introduction''' ==		== '''Introduction''' ==

Jma at 18:33, 3 November 2009

2009-11-03T18:33:53Z

← Older revision		Revision as of 18:33, 3 November 2009
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	== '''Introduction''' ==		='''MolProbity Server''=
			== '''Introduction''' ==

	The MolProbity server, developed by the Richardson group (Ref. 1,2), is a site for the evaluation of single X-ray structures and NMR structure ensembles.  The server performs a number of validations including all-residue Ramachandran analysis, rotamer analysis, and all-atom clash analysis.  Like the PSVS server, the MolProbity server is a valuable structure validation tool in the final stages of structure refinement.  Structures and various metrics are visualized in the KiNG tool, and all analyses and “kinemages” can be downloaded.   The server can be accessed at: [http://molprobity.biochem.duke.edu/ http://molprobity.biochem.duke.edu/].		The MolProbity server, developed by the Richardson group (Ref. 1,2), is a site for the evaluation of single X-ray structures and NMR structure ensembles.  The server performs a number of validations including all-residue Ramachandran analysis, rotamer analysis, and all-atom clash analysis.  Like the PSVS server, the MolProbity server is a valuable structure validation tool in the final stages of structure refinement.  Structures and various metrics are visualized in the KiNG tool, and all analyses and “kinemages” can be downloaded.   The server can be accessed at: [http://molprobity.biochem.duke.edu/ http://molprobity.biochem.duke.edu/].

	== '''Using MolProbity server''' ==		== '''Using MolProbity server''' ==

	=== Uploading a PDB ===		=== Uploading a PDB ===

	PDB files are quickly uploaded, and in the case of NMR ensembles, divided into individual PDB files.  One next analyzes all-atom contacts and geometry (Figure 1).  There is also an “add hydrogens” tool for X-ray structures, which is useful for comparison of NMR/X-ray structure pairs.		PDB files are quickly uploaded, and in the case of NMR ensembles, divided into individual PDB files.  One next analyzes all-atom contacts and geometry (Figure 1).  There is also an “add hydrogens” tool for X-ray structures, which is useful for comparison of NMR/X-ray structure pairs.

	===== Figure 1:  File upload and analysis options in MolProbity =====		===== Figure 1:  File upload and analysis options in MolProbity =====

	[[Image:~~MolProbity_upload~~.png\|1000x500px]]		[[Image:MolProbity upload.png\|1000x500px]]

	=== Structure Analysis in KiNG ===		=== Structure Analysis in KiNG ===

	Structures can be analyzed using the interactive 3D software package KiNG (Figure 2).   The kinemage files feature various structure validation metrics mapped onto the structures(s), including close contacts (pink dots), Ramachandran outliers (green lines) and bad rotamers (yellow side chains).		Structures can be analyzed using the interactive 3D software package KiNG (Figure 2).   The kinemage files feature various structure validation metrics mapped onto the structures(s), including close contacts (pink dots), Ramachandran outliers (green lines) and bad rotamers (yellow side chains).

	===== Figure 2:  Interactive structure analysis in KiNG<br> =====		===== Figure 2:  Interactive structure analysis in KiNG<br> =====

	[[Image:~~MolProbity_KiNG~~.png\|1000x700px]]		[[Image:MolProbity KiNG.png\|1000x700px]]

	For NMR structure ensembles, violations can be viewed for each residue in each structure in a multichart format (Figure 3).		For NMR structure ensembles, violations can be viewed for each residue in each structure in a multichart format (Figure 3).

	===== Figure 3:  Multi-chart analysis of outliers and clashes<br> =====		===== Figure 3:  Multi-chart analysis of outliers and clashes<br> =====

	[[Image:~~MolProbity_multichart~~.png\|1000x750px]]		[[Image:MolProbity multichart.png\|1000x750px]]

	A gzipped kinemage file can be downloaded for archiving and future analysis. The stand-alone version of the KiNG program can be downloaded at: [http://kinemage.biochem.duke.edu/ http://kinemage.biochem.duke.edu/].<br>		A gzipped kinemage file can be downloaded for archiving and future analysis. The stand-alone version of the KiNG program can be downloaded at: [http://kinemage.biochem.duke.edu/ http://kinemage.biochem.duke.edu/].<br>

	=== Ramachandran Analysis ===		=== Ramachandran Analysis ===

	The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: [[Media:2KIF-rama.pdf\|2KIF-rama.pdf]].<br>		The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: [[Media:2KIF-rama.pdf\|2KIF-rama.pdf]].<br>

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

	1.    Davis, I.W., Leaver-Fay, A., Chen, V.B., Block, J.N., Kapral, G.J., Wang, X., Murray, L.W., Arendall III, W.B., Snoeyink, J., Richardson, J.S. and Richardson, D.C. (2007) MolProbity:  all-atom contacts and structure validation for proteins and nucleic acids. ''Nucleic Acids Res. 35'', W375-W383.<br>2.    Lovell, S.C., Davis, I.W., Arendall III, W.B., de Bakker, P.I.W., Word, J.M., Prisant, M.G., Richardson, J.S. and Richardson, D.C. (2003) Structure validation by Cα geometry: φ, ψ, and Cβ deviation.  ''Proteins 50'', 437-450.		1.    Davis, I.W., Leaver-Fay, A., Chen, V.B., Block, J.N., Kapral, G.J., Wang, X., Murray, L.W., Arendall III, W.B., Snoeyink, J., Richardson, J.S. and Richardson, D.C. (2007) MolProbity:  all-atom contacts and structure validation for proteins and nucleic acids. ''Nucleic Acids Res. 35'', W375-W383.<br>2.    Lovell, S.C., Davis, I.W., Arendall III, W.B., de Bakker, P.I.W., Word, J.M., Prisant, M.G., Richardson, J.S. and Richardson, D.C. (2003) Structure validation by Cα geometry: φ, ψ, and Cβ deviation.  ''Proteins 50'', 437-450.


			<br>

	--JimAramini - 02 Nov 2009<br><br>		--JimAramini - 02 Nov 2009<br><br>

Jma at 22:49, 2 November 2009

2009-11-02T22:49:28Z

← Older revision		Revision as of 22:49, 2 November 2009
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	=== Ramachandran Analysis ===		=== Ramachandran Analysis ===

	The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: [[2KIF-rama.pdf]].<br>		The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: [[Media:2KIF-rama.pdf\|2KIF-rama.pdf]].<br>

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

Jma at 22:48, 2 November 2009

2009-11-02T22:48:01Z

← Older revision		Revision as of 22:48, 2 November 2009
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	=== Ramachandran Analysis ===		=== Ramachandran Analysis ===

	The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: [[~~Image:2KIF-rama.pdf\|~~2KIF-rama.pdf]].<br>		The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: [[2KIF-rama.pdf]].<br>

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

Jma at 22:45, 2 November 2009

2009-11-02T22:45:17Z

← Older revision		Revision as of 22:45, 2 November 2009
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	=== Ramachandran Analysis ===		=== Ramachandran Analysis ===

	The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: [[~~image~~:2KIF-rama.pdf\|~~Example Ramachandran output~~]].<br>		The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: [[Image:2KIF-rama.pdf\|2KIF-rama.pdf]].<br>

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

Jma at 22:44, 2 November 2009

2009-11-02T22:44:37Z

← Older revision		Revision as of 22:44, 2 November 2009
Line 31:		Line 31:
	=== Ramachandran Analysis ===		=== Ramachandran Analysis ===

	The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: ~~{{pdf~~:2KIF-rama.pdf\|Example Ramachandran output}}.<br>		The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file.  Here is an example Ramachandran output file: [[image:2KIF-rama.pdf\|Example Ramachandran output]].<br>

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