MolProbity - Revision history

Eric Martz at 19:06, 13 June 2012

2012-06-13T19:06:47Z

← Older revision		Revision as of 19:06, 13 June 2012
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	[[Image:MolProbity_Logo_610x300_Wbkg.jpg\|thumb\|left\|120px\|]]		[[Image:MolProbity_Logo_610x300_Wbkg.jpg\|thumb\|left\|120px\|]]
	[[Image:Validation_outlier_legend.jpg\|thumb\|right\|280px\|Graphical validation icons in MolProbity]]		[[Image:Validation_outlier_legend.jpg\|thumb\|right\|280px\|Graphical validation icons in MolProbity]]
	'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909042073</ref> is a free web service for validation of 3D atomic models of macromolecules produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and make most of the molecular contacts. The local packing evaluation is supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure at right.		'''[http://molprobity.biochem.duke.edu/ MolProbity]'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909042073</ref> is a free web service for validation of 3D atomic models of macromolecules produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and make most of the molecular contacts. The local packing evaluation is supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure at right.

	==All-Atom Contacts==		==All-Atom Contacts==

Eric Martz: /* See Also */

2012-06-13T19:04:24Z

Eric Martz: /* MolProbity Score and Percentiles */

2012-06-13T19:04:08Z

MolProbity Score and Percentiles

← Older revision		Revision as of 19:04, 13 June 2012
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	==MolProbity Score and Percentiles==		==MolProbity Score and Percentiles==

			==See Also==
			[[Quality assessment for molecular models]]

	==References==		==References==
	<references/>		<references/>

Jane S. Richardson: format

2012-06-09T16:37:44Z

format

← Older revision		Revision as of 16:37, 9 June 2012
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	[[Image:MolProbity_Logo_610x300_Wbkg.jpg\|thumb\|left\|120px\|]]		[[Image:MolProbity_Logo_610x300_Wbkg.jpg\|thumb\|left\|120px\|]]
	[[Image:Validation_outlier_legend.jpg\|thumb\|right\|~~240px~~\|Graphical validation icons in MolProbity]]		[[Image:Validation_outlier_legend.jpg\|thumb\|right\|280px\|Graphical validation icons in MolProbity]]
	'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909042073</ref> is a free web service for validation of 3D atomic models of macromolecules produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and make most of the molecular contacts. The local packing evaluation is supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure at right.		'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909042073</ref> is a free web service for validation of 3D atomic models of macromolecules produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and make most of the molecular contacts. The local packing evaluation is supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure at right.

Jane S. Richardson: more concise intro

2012-06-09T16:35:30Z

more concise intro

← Older revision		Revision as of 16:35, 9 June 2012
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	[[Image:MolProbity_Logo_610x300_Wbkg.jpg\|thumb\|left\|120px\|]]		[[Image:MolProbity_Logo_610x300_Wbkg.jpg\|thumb\|left\|120px\|]]
	[[Image:Validation_outlier_legend.jpg\|thumb\|right\|240px\|Graphical validation icons in MolProbity]]		[[Image:Validation_outlier_legend.jpg\|thumb\|right\|240px\|Graphical validation icons in MolProbity]]
	'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909042073</ref> is a web service for validation of 3D atomic models of macromolecules ~~(protein, RNA, etc)~~ produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and ~~over 1/3 in nucleic acids, and they~~ make most of the molecular contacts. ~~Those~~ local packing ~~criteria are~~ supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.		'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909042073</ref> is a free web service for validation of 3D atomic models of macromolecules produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and make most of the molecular contacts. The local packing evaluation is supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure at right.

	==All-Atom Contacts==		==All-Atom Contacts==

Jane S. Richardson: format, headings

2012-06-09T16:29:43Z

format, headings

@@ Line 1: / Line 1: @@
-[[Image:MolProbity_Logo_610x300_Wbkg.jpg|thumb|right|240px|]]
+[[Image:MolProbity_Logo_610x300_Wbkg.jpg|thumb|left|120px|]]
 [[Image:Validation_outlier_legend.jpg|thumb|right|240px|Graphical validation icons in MolProbity]]
-'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909054481</ref> is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR).  Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>.  The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and over 1/3 in nucleic acids, and they make most of the molecular contacts. Those local packing criteria are supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.
+'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909042073</ref> is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR).  Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>.  The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and over 1/3 in nucleic acids, and they make most of the molecular contacts. Those local packing criteria are supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.

Jane S. Richardson: added image

2012-06-09T16:17:16Z

added image

← Older revision		Revision as of 16:17, 9 June 2012
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	[[Image:Validation_outlier_legend.jpg\|thumb\|right\|240px\|~~Key to graphical~~ validation icons ~~used~~ in MolProbity]]		[[Image:MolProbity_Logo_610x300_Wbkg.jpg\|thumb\|right\|240px\|]]
			[[Image:Validation_outlier_legend.jpg\|thumb\|right\|240px\|Graphical validation icons in MolProbity]]
	'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909054481</ref> is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and over 1/3 in nucleic acids, and they make most of the molecular contacts. Those local packing criteria are supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.		'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909054481</ref> is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and over 1/3 in nucleic acids, and they make most of the molecular contacts. Those local packing criteria are supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.

Jane S. Richardson at 14:57, 9 June 2012

2012-06-09T14:57:59Z

← Older revision		Revision as of 14:57, 9 June 2012
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	[[Image:Validation_outlier_legend.jpg\|thumb\|right\|Key to graphical validation icons used in MolProbity]]		[[Image:Validation_outlier_legend.jpg\|thumb\|right\|240px\|Key to graphical validation icons used in MolProbity]]
	'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909054481</ref> is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and over 1/3 in nucleic acids, and they make most of the molecular contacts. Those local packing criteria are supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.		'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909054481</ref> is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and over 1/3 in nucleic acids, and they make most of the molecular contacts. Those local packing criteria are supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.

Jane S. Richardson: more text, image

2012-06-09T14:51:21Z

more text, image

← Older revision		Revision as of 14:51, 9 June 2012
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	'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909054481</ref> is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. It produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.		[[Image:Validation_outlier_legend.jpg\|thumb\|right\|Key to graphical validation icons used in MolProbity]]
			'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909054481</ref> is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. The contact analysis is both sensitive and powerful because the H's are about half the atoms in a protein and over 1/3 in nucleic acids, and they make most of the molecular contacts. Those local packing criteria are supplemented with updated versions of traditional validation criteria such as Ramachandran, rotamer, and covalent-geometry measures, and a few new criteria for RNA structure. MolProbity produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.

Jane S. Richardson: started page

2012-06-09T14:05:40Z

started page

New page

'''MolProbity'''<ref>doi:10.1093/nar/gkh398</ref><ref>doi:10.1093/nar/gkm216</ref><ref name="Chen2010">doi: 10.1107/S0907444909054481</ref> is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program<ref name="Reduce">doi:10.1006/jmbi.1998.2401</ref> and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe<ref name="Probe">doi: 10.1006/jmbi.1998.2400</ref>. It produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.

← Older revision		Revision as of 19:04, 13 June 2012
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	==See Also==		==See Also==
	[[Quality assessment for molecular models]]		*[[Quality assessment for molecular models]]

	==References==		==References==
	<references/>		<references/>