MolProbity

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Graphical validation icons in MolProbity
Graphical validation icons in MolProbity

MolProbity[1][2][3] 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[4] and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe[5]. 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.

Contents

All-Atom Contacts

Conformational Criteria

Ramachandran

Sidechain Rotamers

RNA Backbone Conformers & Ribose Puckers

Geometrical Criteria

Bond Lengths & Angles

Cβ Deviations

MolProbity Score and Percentiles

See Also

References

  1. ↑ Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W615-9. PMID:15215462 doi:10.1093/nar/gkh398
  2. ↑ Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB 3rd, Snoeyink J, Richardson JS, Richardson DC. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83. Epub 2007 Apr 22. PMID:17452350 doi:10.1093/nar/gkm216
  3. ↑ Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21. Epub 2009 Dec 21. PMID:20057044 doi:10.1107/S0907444909042073
  4. ↑ Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol. 1999 Jan 29;285(4):1735-47. PMID:9917408 doi:10.1006/jmbi.1998.2401
  5. ↑ Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol. 1999 Jan 29;285(4):1711-33. PMID:9917407 doi:10.1006/jmbi.1998.2400

Proteopedia Page Contributors and Editors (what is this?)

Jane S. Richardson, Eric Martz

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