MolProbity: Difference between revisions

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[[Image:MolProbity_Logo_610x300_Wbkg.jpg|thumb|left|120px|]]

[[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==

MolProbity: Difference between revisions

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 [[Image:MolProbity_Logo_610x300_Wbkg.jpg|thumb|left|120px|]]
 [[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==