Nucleic Acids Research Advance Access originally published online on November 3, 2008
Nucleic Acids Research 2009 37(Database issue):D436-D442; doi:10.1093/nar/gkn840
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Nucleic Acids Research, 2009, Vol. 37, Database issue D436-D442
© 2008 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.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
VIPERdb2: an enhanced and web API enabled relational database for structural virology
1Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 and 2Department of Chemistry, Biophysics Program, 930 N. University Ave., University of Michigan, Ann Arbor, MI 48109, USA
*To whom correspondence should be addressed. Tel: +1 858 784 8191; Fax: +1 858 784 8660; Email: reddyv{at}scripps.edu
Received September 15, 2008. Revised October 13, 2008. Accepted October 14, 2008.
VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb2, we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as 
–
(Phi–Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence–structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.