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

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      Abstract

      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.

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      Most cited references 43

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      Coot: model-building tools for molecular graphics.

      CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.
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        The Protein Data Bank.

        The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
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          PROCHECK: a program to check the stereochemical quality of protein structures

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            Author and article information

            Affiliations
            1Department of Biochemistry, Duke University, Durham, NC, USA and 2Department of Computer Science, UNC Chapel Hill, Chapel Hill, NC, USA
            Author notes
            *To whom correspondence should be addressed. +1-919-684-6010 dcr@ 123456kinemage.biochem.duke.edu
            Journal
            Nucleic Acids Res
            Nucleic Acids Res
            nar
            nar
            Nucleic Acids Research
            Oxford University Press
            0305-1048
            1362-4962
            July 2007
            22 April 2007
            22 April 2007
            : 35
            : Web Server issue
            : W375-W383
            17452350
            1933162
            10.1093/nar/gkm216
            © 2007 The Author(s)

            This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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            Genetics

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