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Comprehensive help and frequently asked questions

VAST Search

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VAST Search Help

Help on submitting VAST Searches


More help on VAST Search

Linking to VAST

direct WWW access to the VAST server


non-redundant protein structure subsets


NCBI's structure database


Taxonomy in MMDB

Cn3D v4.1

3D-structure viewer


Research topics and staff

Vector Alignment Search Tool

Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one. From the MMDB Structure summary pages, retrieved via Entrez, structure neighbors are available for protein chains and individual structural domains. If you already know a PDB/MMDB-Id you can try this at once, using the input form in the right column.

On the Structure summary page, use "3d Domains" or "Protein" to retrieve a list of similar structures. For example, click on a bar with a chain identifier such as "B", or the bar below the Chain B with a domain identifier such as "1" , to get a list of neighbors. The results of the precompiled VAST search will then present structural neighbors graphically. Using the check boxes in the leftmost column of this graph, select those structures you would like to see superimposed and click on "View 3D Structure" to view these with the mime-typed helper application you have installed (e.g., Cn3D).

VAST Search is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user. This service is meant to be used with newly determined protein structures that are not yet part of MMDB. Structure neighbors for proteins already in MMDB have been pre-computed and can simply be looked up from MMDB's Structure summary pages!

For more help on using VAST and VAST Search, follow the related links on this page.

Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol 1996 Jun; 6(3):377-385.

Madej T, Gibrat JF, Bryant SH. (1995) Threading a database of protein cores. Proteins 1995 Nov; 23(3):356-3690.


Structure Summary via




Install and test structure alignment viewers:

Get Cn3D v4.1 and look at this example to test!

Read a bit more about VAST...

Updated 06/21/04

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