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2015 ; 190
(1
): 47-55
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CapsidMaps: protein-protein interaction pattern discovery platform for the
structural analysis of virus capsids using Google Maps
#MMPMID25697908
Carrillo-Tripp M
; Montiel-García DJ
; Brooks CL 3rd
; Reddy VS
J Struct Biol
2015[Apr]; 190
(1
): 47-55
PMID25697908
show ga
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 ?-? 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.