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Title: MolProbity: all-atom structure validation for macromolecular crystallography

Abstract

MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction. MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. Itmore » is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.« less

Authors:
; ; ; ; ; ; ; ;  [1]
  1. Department of Biochemistry, Duke University, Durham, NC 27710 (United States)
Publication Date:
OSTI Identifier:
22347925
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 66; Journal Issue: Pt 1; Other Information: PMCID: PMC2803126; PMID: 20057044; PUBLISHER-ID: dz5180; OAI: oai:pubmedcentral.nih.gov:2803126; Copyright (c) Chen et al. 2010; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; CHAINS; CRYSTAL STRUCTURE; CRYSTALLIZATION; CRYSTALLOGRAPHY; CRYSTALS; DIAGRAMS; ERRORS; HYDROGEN; SOLIDS; SPECTRA; TORSION; VALIDATION

Citation Formats

Chen, Vincent B., Arendall, W. Bryan III, Headd, Jeffrey J., Keedy, Daniel A., Immormino, Robert M., Kapral, Gary J., Murray, Laura W., Richardson, Jane S., and Richardson, David C., E-mail: dcr@kinemage.biochem.duke.edu. MolProbity: all-atom structure validation for macromolecular crystallography. Denmark: N. p., 2010. Web. doi:10.1107/S0907444909042073.
Chen, Vincent B., Arendall, W. Bryan III, Headd, Jeffrey J., Keedy, Daniel A., Immormino, Robert M., Kapral, Gary J., Murray, Laura W., Richardson, Jane S., & Richardson, David C., E-mail: dcr@kinemage.biochem.duke.edu. MolProbity: all-atom structure validation for macromolecular crystallography. Denmark. doi:10.1107/S0907444909042073.
Chen, Vincent B., Arendall, W. Bryan III, Headd, Jeffrey J., Keedy, Daniel A., Immormino, Robert M., Kapral, Gary J., Murray, Laura W., Richardson, Jane S., and Richardson, David C., E-mail: dcr@kinemage.biochem.duke.edu. Fri . "MolProbity: all-atom structure validation for macromolecular crystallography". Denmark. doi:10.1107/S0907444909042073.
@article{osti_22347925,
title = {MolProbity: all-atom structure validation for macromolecular crystallography},
author = {Chen, Vincent B. and Arendall, W. Bryan III and Headd, Jeffrey J. and Keedy, Daniel A. and Immormino, Robert M. and Kapral, Gary J. and Murray, Laura W. and Richardson, Jane S. and Richardson, David C., E-mail: dcr@kinemage.biochem.duke.edu},
abstractNote = {MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction. MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.},
doi = {10.1107/S0907444909042073},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
number = Pt 1,
volume = 66,
place = {Denmark},
year = {Fri Jan 01 00:00:00 EST 2010},
month = {Fri Jan 01 00:00:00 EST 2010}
}
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