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Nucleic Acids Research 2006 34(Database Issue):D386-D389; doi:10.1093/nar/gkj032
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Nucleic Acids Research, 2006, Vol. 34, Database issue D386-D389
© The Author 2006. Published by Oxford University Press. All rights reserved
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 for non-commercial purposes 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. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

VIPERdb: a relational database for structural virology

Craig M. Shepherd, Ian A. Borelli, Gabriel Lander, Padmaja Natarajan, Vinay Siddavanahalli1, Chandrajit Bajaj1, John E. Johnson, Charles L. Brooks, III and Vijay S. Reddy*

Department of Molecular Biology, TPC-6 The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037, USA 1Computational Visualization Center, University of Texas at Austin Austin, TX 78712, USA

*To whom correspondence should be addressed. Tel: +1 858 784 8191; Fax: +1 858 784 8688; Email: reddyv{at}scripps.edu

Received August 31, 2005. Accepted September 23, 2005.

VIPERdb (http://viperdb.scripps.edu) is a database for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the structural virology community, with an emphasis on the description and comparison of derived data from structural and energetic analyses of capsids. A relational database implementation based on a schema for macromolecular structure makes the data highly accessible to the user, allowing detailed queries at the atomic level. Together with curation practices that maintain data uniformity, this will facilitate structural bioinformatics studies of virus capsids. User friendly search, visualization and educational tools on the website allow both structural and derived data to be examined easily and extensively. Links to relevant literature, sequence and taxonomy databases are provided for each entry.


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