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

Abstract

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.

Figure 1.

(a) Info-page of Black Beetle Virus (PDB ID 2bbv). (b) Default view of the Φ–Ψ Explorer Tab. See text for details.

Figure 2.

(a) Φ–Ψ Map of the interface residues of the Black Beetle Virus (PDB ID 2bbv) in the Q3F view, showing all the methionine residues color coded according to its sequence conservation (conserved among all nodaviruses are shown in red, ‘Hot Spots’). Residue 182 of the B subunit is selected. (b) Protein structure in Cartesian space of the asymmetric unit, color coded according to subunit name (A: blue, B: red, C: green) and using the ‘trace' representation. Residues are automatically displayed in the IAU tab, when they are selected in the Φ–Ψ map. See text for details.