Vijay Reddy
 Jack Johnson
 Charles Brooks
 Florence Tama

VIrus Particle ExploreR(VIPER)db is a repository of virus capsid structures available in the Protein Databank (PDB) and also a relational database for informatics in structural virology. Multiscale modeling tools have been developed to analyze protein-protein interactions, viral surfaces, energetics, assembly pathways, capsid dynamics and aspects of chemical biology in viruses. The results are used to annotate results from X-ray crystallography and molecular virology. Currently, all of the viral capsids are oriented in a single icosahedral convention. The coordinates and the derived results are integrated into a relational database

Shown below is a gallery of the biggest virus structures available in the databse


There are currently 81 unique entries (200 in total) from 23 different families and 35 genera in the database. Each entry is described in terms of its structure, at different levels of organization, related information on capsid size, T number, and with links to primary sequence data in SWISS-PROT/GENBANK databases. Additionally, each capsid is annotated through the description of the residue pairs contacting at protein-protein interfaces, buried surface areas, solvation energies, association energies and exposed surface residues as derived from computational analysis.

Shown below is a ribbon diagram of the canonical beta-barrel motif seen in the majority of viral capsids.


A number of server-side web based tools and utilites for structural analysis, visualization of virus structures and to query the database are avialble at the VIPERdb site.