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VIPERdb: A Tool for Virus Research.

Phuong T Ho1, Daniel J Montiel-Garcia1,2, Jonathan J Wong1

  • 1Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA;

Annual Review of Virology
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PubMed
Summary

The VIrus Particle ExploreR database (VIPERdb) offers comprehensive structural data and analysis tools for icosahedral and helical viruses. It facilitates structure-based bioinformatics analysis of virus capsids with integrated visualization and comparison tools.

Keywords:
VIPER databaseVIPERdbcapsid proteinscapsid structurestructure-derived propertiesvirus structure

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Area of Science:

  • Structural Biology
  • Virology
  • Bioinformatics

Background:

  • Virus capsid structures are crucial for understanding viral assembly, function, and therapeutic targeting.
  • Existing databases often lack comprehensive integration of structural data with analysis and visualization tools.

Purpose of the Study:

  • To provide an updated overview of the VIrus Particle ExploreR database (VIPERdb).
  • To highlight the integrated structure-derived information, visualization, and analysis tools for virus capsids.
  • To showcase the expansion of VIPERdb to include helical viruses and non-icosahedral capsids.

Main Methods:

  • Data curation and analysis procedures were modified to include helical viruses and non-icosahedral capsids.
  • Integration of structure-derived attributes such as size, T number, genome type, and surface residues.
  • Development of web-based tools for interactive structure exploration and comparative analysis.

Main Results:

  • VIPERdb provides comprehensive structure-derived information on icosahedral and now helical viruses and non-icosahedral capsids.
  • Integrated visualization tools, including JavaScript charting libraries, enable trend exploration.
  • Web interfaces offer tools for comparing virus capsid properties and facilitating bioinformatics analysis.

Conclusions:

  • VIPERdb serves as a valuable resource for structure-based bioinformatics analysis of virus capsids.
  • The database facilitates deeper insights into viral structure-function relationships.
  • Continuous updates and expansion enhance VIPERdb's utility for virology research.