VIPERdb2: an enhanced and web API enabled relational database for structural virology.

Authors:
Dr. Mauricio Carrillo-Tripp, PhD
Dr. Mauricio Carrillo-Tripp, PhD
Biomolecular Diversity Laboratory, Cinvestav
Principal Investigator
Computational Biophysics
Monterrey, NL | Mexico
Ian A Borelli
Ian A Borelli
TPC-6 The Scripps Research Institute
United States
Gabriel Lander
Gabriel Lander
The Scripps Research Institute
Padmaja Natarajan
Padmaja Natarajan
Joint Center for Structural Genomics
John E Johnson
John E Johnson
The Scripps Research Institute
United States
Charles L Brooks
Charles L Brooks
University of Michigan
United States

Nucleic Acids Res 2009 Jan 3;37(Database issue):D436-42. Epub 2008 Nov 3.

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

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, VIPERdb(2), 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 (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.

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http://dx.doi.org/10.1093/nar/gkn840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686430PMC
January 2009
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