Skip Navigation

VIPERdb


NAR Molecular Biology Database Collection entry number 761
Shepherd, C.M., Borelli, I.A., Lander, G., Natarajan, P., Siddavanahalli, V.1, Bajaj, C.1, Johnson, J.E., Brooks III, C.L., Reddy, V.S.
Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92130-1000
1Computational Visualization Center, University of Texas at Austin, Austin, TX, 78712-0027, USA

Database Description

VIPERdb is a database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and energetic analyses on these systems, and high quality renderings for visual exploration. In addition, all virus capsids are placed in a single orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities, links to other relevant databases, background information on virus capsid structure, and useful tools like the ¡ÈOligomer Generator¡É, which generates full or partial capsid structure from the deposited asymmetric unit. VIPERdb is accessible from http://viperdb.scripps.edu.

Recent Developments

VIPERdb is a relational database implementation of the original VIPER resource, based on the mmCIF format for macromolecular structure. Concomitant to the database migration, the resource has undergone a significant expansion to include all icosahedral virus capsid structures in the PDB, for a current total of 223 entries representing 27 families and 40 genera. Significant improvements have been made in the presentation of derived data from structural and energetic analyses on virus capsids at the web site. Quantities calculated at the residue level are shown in interactive graphs with zoom capabilities and helpful mouseover pop-ups. Other data items in tables are linked to graphics and/or VRML objects displaying the structures and interactions involved. Users can now explore the database structure and make sophisticated queries using the ¡ÈDatabase Browser¡É, with results being returned in a variety of formats. The derived data can be explored according to a number of criteria (e.g. residue type, virus family) using the ¡ÈContact Finder¡É and ¡ÈAmino Acid Info¡É tools. Users can also convert their own structures to the VIPER orientation convention using the PDB-to-VIPER tool, and can even submit structures in progress to the VIPERdb Analysis Database: all the in-house analyses will be performed on their structure and made available to them on the web site. As an introduction to new users, an interactive tour of the web site highlighting the recent developments mentioned above has been made available at http://viperdb.scripps.edu/tour.php.

Acknowledgements

VIPERdb is a training/service and dissemination component of the NIH Research Resource: Multiscale Modeling Tools for Structural Biology (MMTSB), which is fully funded by the National Center for Research Resources of the National Institutes of Health (RR12255).

Subcategory: Protein structure
Subcategory: Viral genome databases

Go to the abstract in the NAR 2006 Database Issue.
Oxford University Press is not responsible for the content of external internet sites