MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
Department of Biochemistry, Duke University, Durham, NC 27710-3711, USA
* To whom correspondence should be addressed: Tel: +1 919 684 6010; Fax: +1 919 684 8885; Email: dcr{at}kinemage.biochem.duke.edu
Received February 20, 2004; Revised and Accepted March 25, 2004
MOLPROBITY is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules and 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. The results are reported in multiple forms: as overall numeric scores, as lists, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown on-line in the KING viewer. This service is available free to all users at http://kinemage.biochem.duke.edu.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.
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