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VIPERdb Utilities

Here you can find links to many tools and utilities VIPERdb offers in order to further analyze and view the data found within this site.


The Matrices:

Apply these coordinate matrices to the icosahedral asymmetric subunit of a virus in order to create the entire capsid. You can use all 60 matrices, or select the matrices that correspond to the T-number of a particular virus.

Oligomer
Generator:

Create either part or all of a virus capsid from a given virus subunit.

Icosahedral
Server

Detailed information regarding the construction of icosahedra using different quasi-equivalent surfaces lattices, as well as downloadable projection files of the icosahedra.

Icosahedron Generator

An interactive java based tool created by using the information in the Icosahderal server

Map a
Residue:

Select a particular residue and view its location in the protein structure using the Virtual Reality Markup Language viewer.

Viper Analysis:

Submit your structure coordinates for VIPERdb analysis.

View Virus Gallery:

This tool generates galleries of particular types of images available in the VIPERdb for a group of capsids within and between families/genera, which can be further ordered by their size. This tool replaces the "visual_viper" tool.

Contact Finder:

Contact finder is a new utility that extracts chosen types residue pairs (e.g., ALA-PHE, ASP-LYS ..)from the VIPERdb database that are in contact at the subunit interfaces and within the specified distance limits. The search can be tailored to a particular virus/genus/family.

Amino Acid Information:

Returns contact and association energy information for a particular amino acid within a capsid.




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