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J Struct Biol. 2015 Apr;190(1):47-55. doi: 10.1016/j.jsb.2015.02.003. Epub 2015 Feb 16.

CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps.

Author information

1
Biomolecular Diversity Laboratory, Unidad de Genómica Avanzada (Langebio) CINVESTAV, Irapuato, Mexico. Electronic address: trippm@langebio.cinvestav.mx.
2
Biomolecular Diversity Laboratory, Unidad de Genómica Avanzada (Langebio) CINVESTAV, Irapuato, Mexico.
3
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
4
Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.

Abstract

Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the φ-ψ Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu.

KEYWORDS:

Heat maps; Quaternary interactions; Similarity score; Viral capsids; Web interface

PMID:
25697908
PMCID:
PMC4750372
DOI:
10.1016/j.jsb.2015.02.003
[Indexed for MEDLINE]
Free PMC Article

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