J Struct Biol 2015 Apr 16;190(1):47-55. Epub 2015 Feb 16.
Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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Nucleic Acids Res 2009 Jan 3;37(Database issue):D436-42. Epub 2008 Nov 3.
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Read More
Proteins 2008 Nov;73(3):644-55
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
Viral capsids are composed of multiple copies of one or a few chemically distinct capsid proteins and are mostly stabilized by inter subunit protein-protein interactions. There have been efforts to identify and analyze these protein-protein interactions, in terms of their extent and similarity, between the subunit interfaces related by quasi- and icosahedral symmetry. Here, we describe a new method to map quaternary interactions in spherical virus capsids onto polar angle space with respect to the icosahedral symmetry axes using azimuthal orthographic diagrams. Read More
Nucleic Acids Res 2006 Jan;34(Database issue):D386-9
Department of Molecular Biology, TPC-6 The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
VIPERdb (http://viperdb.scripps.edu) is a database for icosahedral virus capsid structures. Read More
J Mol Biol 2015 Nov 12;427(22):3613-3624. Epub 2015 Sep 12.
Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109-2218, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Biophysics Program, University of Michigan, Ann Arbor, MI 48109-1055, USA. Electronic address:
Viral capsids exhibit elaborate and symmetrical architectures of defined sizes and remarkable mechanical properties not seen with cellular macromolecular complexes. Given the uniqueness of the higher-order organization of viral capsid proteins in the virosphere, we explored the question of whether the patterns of protein-protein interactions within viral capsids are distinct from those in generic protein complexes. Our comparative analysis involving a non-redundant set of 551 inter-subunit interfaces in viral capsids from VIPERdb and 20,014 protein-protein interfaces in non-capsid protein complexes from the Protein Data Bank found 418 generic protein-protein interfaces that share similar physicochemical patterns with some protein-protein interfaces in the capsid set, using the program PCalign we developed for comparing protein-protein interfaces. Read More