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Comprehensive help and frequently asked questions Submit structure database searches Help on submitting VAST Searches More help on VAST Search direct WWW access to the VAST server non-redundant protein structure subsets NCBI's structure database 3D-structure viewer Research topics and staff |
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).
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. |
      Install and test structure alignment viewers: Get Cn3D v4.1 and look at this example to test! |
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Updated 04/24/08 |
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