VIPERdb (https://viperdb.org) is now at the The Hormel Institute.
Latest Entries
- 8fq42023-01-05AAV1 VP3 Only Capsid
- 8f262022-11-07STRUCTURE OF A 60MER DEGP CAGE BOUND TO THE CLIENT PROTEIN HTRF1
- 8h892022-10-22Capsid of Ralstonia phage GP4
- 8eu52022-10-18Acheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure
- 8eu62022-10-18Acheta domesticus segmented densovirus high buoyancy fraction 1 (HB1) empty capsid structure
- 8eu72022-10-18Acheta domesticus segmented densovirus VP-ORF1 virus-like particle
- 8erk2022-10-12Acheta domesticus segmented densovirus, high buoyancy (HB) capsid, a mixed population of empty and immature full particles
Highlights
Featured Reviews and Publications


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.
- Related Publications
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 | |
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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 | |
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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 |