VIPERdb Overview

  • This web site describes the various icosahedral virus capsid structures in the Protein Data Bank (PDB) in terms of their complete capsids, and detailed structural and computational analysis.
  • The protomeric coordinates (asymmetric unit) were transformed and stored in a single icosahedral convention (2(Z)-3-5-(X)2). Coordinates (sometimes) were further processed by rearranging the nucleic acid residues, hetero atoms, and water molecules (if present) at the end of the protein chains for the ease of further analysis.
  • Structures are classified in terms of their quasi-symmetry (e.g. T=3, T=4, T=7) and pseudo-symmetry (e.g., P=3).
  • Tools are being developed to study the capsids in terms of structural, energetic, and assembly aspects. The derived results are made available throught this website.
  • The site is being developed as part of the training, service and dissemination component of the NIH Research Resource: Multiscale Modeling Tools for Structural Biology (MMTSB).
  • You are welcome to download the figures and the data presented at this website. Please cite the reference and the VIPERdb website when you use them in the publications/ posters/ presentations. Thank you for your cooperation.

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