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

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 Φ–Ψ (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.

[1]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[2]  John E. Johnson,et al.  A general method to quantify quasi-equivalence in icosahedral viruses. , 2002, Journal of molecular biology.

[3]  Markus Gruber,et al.  A discrete view on fold space , 2008, Bioinform..

[4]  Cédric Notredame,et al.  3DCoffee: combining protein sequences and structures within multiple sequence alignments. , 2004, Journal of molecular biology.

[5]  Mauricio Carrillo-Tripp,et al.  A novel method to map and compare protein–protein interactions in spherical viral capsids , 2008, Proteins.

[6]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[7]  Manfred J. Sippl,et al.  A note on difficult structure alignment problems , 2008, Bioinform..

[8]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[9]  Christoph Gille,et al.  STRAP: editor for STRuctural Alignments of Proteins , 2001, Bioinform..

[10]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.

[11]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[12]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[13]  Chandrajit L. Bajaj,et al.  VIPERdb: a relational database for structural virology , 2005, Nucleic Acids Res..

[14]  V. Reddy,et al.  Extent of protein–protein interactions and quasi‐equivalence in viral capsids , 2004, Proteins.

[15]  John E. Johnson,et al.  Virus Particle Explorer (VIPER), a Website for Virus Capsid Structures and Their Computational Analyses , 2001, Journal of Virology.

[16]  T. P. Flores,et al.  Multiple protein structure alignment , 1994, Protein science : a publication of the Protein Society.

[17]  A. Konagurthu,et al.  MUSTANG: A multiple structural alignment algorithm , 2006, Proteins.

[18]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[19]  John E. Johnson,et al.  Exploring icosahedral virus structures with VIPER , 2005, Nature Reviews Microbiology.