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Featured Reviews and Publications
- VIPERdb v3. 0: a structure-based data analytics platform for viral capsids.
- VIPERdb: A Tool for Virus Research
- VIPERdb2: an enhanced and web API enabled relational database for structural virology
- CapsidMesh: atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties.
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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.
- 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
|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|
|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 This information is limited and no longer actively maintained.|
|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|