VIPERdb v3.0: a structure-based data analytics platform for viral capsids

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  • Daniel Montiel-Garcia
    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
  • Nelly Santoyo-Rivera
    Departments of Computer Systems and Information Technologies, Tecnologico Nacional de Mexico & Instituto Tecnológico Superior de Irapuato, Irapuato, Guanajuato, México
  • Phuong Ho
    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
  • Mauricio Carrillo-Tripp
    Biomolecular Diversity Laboratory, Centro de Investigación y de Estudios Avanzados Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, C.P. 66600, Apodaca, Nuevo León, México
  • Charles L Brooks III
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
  • John E Johnson
    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
  • Vijay S Reddy
    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA

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<jats:title>Abstract</jats:title> <jats:p>VIrus Particle ExploreR data base (VIPERdb) (http://viperdb.scripps.edu) is a curated repository of virus capsid structures and a database of structure-derived data along with various virus specific information. VIPERdb has been continuously improved for over 20 years and contains a number of virus structure analysis tools. The release of VIPERdb v3.0 contains new structure-based data analytics tools like Multiple Structure-based and Sequence Alignment (MSSA) to identify hot-spot residues within a selected group of structures and an anomaly detection application to analyze and curate the structure-derived data within individual virus families. At the time of this writing, there are 931 virus structures from 62 different virus families in the database. Significantly, the new release also contains a standalone database called ‘Virus World database’ (VWdb) that comprises all the characterized viruses (∼181 000) known to date, gathered from ICTVdb and NCBI, and their capsid protein sequences, organized according to their virus taxonomy with links to known structures in VIPERdb and PDB. Moreover, the new release of VIPERdb includes a service-oriented data engine to handle all the data access requests and provides an interface for futuristic data analytics using machine leaning applications.</jats:p>

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