Structures
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Getting Started

VIPERdb is a web interface for exploring virus structures

We analyze PDB atomic coordinates and provide a collection of useful structure-derived data and web utilities.
Whether you're a veteran virologist or a novice student, you can find resources for both research and learning.

Viper Convention


  • Having a single convention facilitates comparison and analysis across the entire collection of structures
  • Protomeric coordinates (asymmetric units) were transformed and stored in a single icosahedral convention (2(Z)-3-5-(X)2)
  • Structures are classified in terms of their quasi-symmetry (e.g. T=3, T=4, T=7) and pseudo-symmetry (e.g., P=3)
  • Coordinates were sometimes 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

Data

Structure Categories
Family Index Entries grouped by family
Genus Index Entries grouped by genus
T-Number Index Entries grouped by quasi-symmetry
X-Ray Structures Entries structurally determined by x-ray crystallography
Cryo-EM Structures Entries structurally determined by cryogenic electron microscopy
Theoretical Models Homology models
Helical Structures with helical geometry
Other Structures with neither icosahedral nor helical geometry
Miscellaneous Information
Icosahedral Matrices View the 60 matrices that can be used to transform a single asymmetric unit into a complete capsid
Crystal Information Crystallization conditions for viruses, space groups, inter-particle contacts, etc.
Hetero Atoms/Groups A listing of RNA/DNA, water, ions, and other groups in the virus structures ordered alphabetically by virus name. This information is limited and no longer actively maintained.

Utilities

Submit to Viperdb Submit your own structural atomic coordinates for us to analyze
Web API's Use these online scripts to query various data from our database
Family Association Energies View association energies for subunit interfaces for each entry grouped by family
Oligomer Generator Generate oligomers and portions of capsids based on chains and matrix identifiers
Icosahedral Server Follow a walkthrough of how to create your own paper icosahedron from printable hexagonal templates
Gallery Maker Create a gallery of specified images from this site
Contact Finder Extract residue pairs from a capsid that are within a specified distance from each other
Amino Acid Information Retrieve all information for a specific amino acid within a capsid
Secondary Structure Information Display secondary structure information for a range of residues with a capsid

More Help and Information

Info Page Components How they're organized, types of images available, downloadable files, generating custom coordinates, etc.
Calculations How certain data (net surface charge, SASA, etc.) were calculated
Tutorial Videos Information on various VIPERdb features in video format