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Annu Rev Virol. 2018 Sep 29;5(1):477-488. doi: 10.1146/annurev-virology-092917-043405.

VIPERdb: A Tool for Virus Research.

Author information

1
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA; email: reddyv@scripps.edu.
2
Department of Information Technologies, Instituto Tecnológico Superior de Irapuato, 36300 Irapuato, Guanajuato, Mexico.
3
Biomolecular Diversity Laboratory, Centro de Investigación y de Estudios Avanzados Unidad Monterrey, 66600 Apodaca, Nuevo León, Mexico.
4
Department of Computational Medicine and Bioinformatics, Department of Chemistry, and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA.

Abstract

The VIrus Particle ExploreR database (VIPERdb) ( http://viperdb.scripps.edu ) is a database and web portal for primarily icosahedral virus capsid structures that integrates structure-derived information with visualization and analysis tools accessed through a set of web interfaces. Our aim in developing VIPERdb is to provide comprehensive structure-derived information on viruses comprising simple to detailed attributes such as size (diameter), architecture ( T number), genome type, taxonomy, intersubunit association energies, and surface-accessible residues. In addition, a number of web-based tools are provided to enable users to interact with the structures and compare and contrast structure-derived properties between different viruses. Recently, we have constructed a series of data visualizations using modern JavaScript charting libraries such as Google Charts that allow users to explore trends and gain insights based on the various data available in the database. Furthermore, we now include helical viruses and nonicosahedral capsids by implementing modified procedures for data curation and analysis. This article provides an up-to-date overview of VIPERdb, describing various data and tools that are currently available and how to use them to facilitate structure-based bioinformatics analysis of virus capsids.

KEYWORDS:

VIPER database; VIPERdb; capsid proteins; capsid structure; structure-derived properties; virus structure

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