MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

Published

Journal Article

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

Full Text

Duke Authors

Cited Authors

  • Davis, IW; Leaver-Fay, A; Chen, VB; Block, JN; Kapral, GJ; Wang, X; Murray, LW; Arendall, WB; Snoeyink, J; Richardson, JS; Richardson, DC

Published Date

  • July 2007

Published In

Volume / Issue

  • 35 / Web Server issue

Start / End Page

  • W375 - W383

PubMed ID

  • 17452350

Pubmed Central ID

  • 17452350

Electronic International Standard Serial Number (EISSN)

  • 1362-4962

International Standard Serial Number (ISSN)

  • 0305-1048

Digital Object Identifier (DOI)

  • 10.1093/nar/gkm216

Language

  • eng