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VAST: Vector Alignment Search Tool

About VAST

VAST, short for Vector Alignment Search Tool, is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures ("similar structures") by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison.

Find similarly shaped
protein molecules or 3D domains   The original VAST finds structures that are similar to individual protein molecules, or individual 3D domains, in your query structure, as shown in the illustrated example on this page. The original VAST help document, and an annotated example of the original-style VAST display, provide additional details. (While the new style, VAST+ search results are displayed by default, the original VAST results can be viewed by clicking on the "Original VAST" button on any VAST+ search results page. Read more about the difference between VAST and VAST+.)

Find similarly shaped
macromolecular complexes   An enhanced resource, VAST+, is also available, and finds structures that are similar to your query structure's macromolecular complex ( biological unit). The VAST+ help document provides additional details, including illustrated examples of search results for glutamate dehydrogenase (Thermotoga maritima) and deoxyhemoglobin (Homo sapiens). (Read more about the difference between VAST and VAST+.)

Retrieve pre-computed results   VAST and VAST+ are applied on every protein in the Molecular Modeling Database (MMDB) during MMDB data processing in order to identify similar 3D structures.

To retrieve the pre-computed results, follow the "Similar Structures" link on a structure's summary page, or simply enter your query structure's MMDB ID or PDB ID below and press "GO."

Show Similar Structures for:
The VAST+ results are shown by default. If you prefer to view the original-style VAST display, click on the "Original VAST" button on any VAST+ search results page. (Read more about the difference between VAST and VAST+.)
Search with a new structure
(PDB formatted file)   If you have a newly resolved protein structure that is not yet in MMDB, then you can use the VAST Search service to input your data in PDB file format and compare your structure against all those in MMDB. The VAST Search Help document provides additional information about using the VAST Search page. (Please note that, at this time, VAST Search still returns results in the original-style VAST display, listing structures that have similarities to individual protein molecules in your query structure. Although some of the returned structures might also have a biological unit that is similar to the query, the original style VAST results does not group results by biological unit similarity.)
View 3D structures and superpositions   Whether you retrieve similar structures from the summary page of a publicly available structure or through VAST Search, you can then use the free Cn3D structure viewing program to view a superposition of the query structure and similar structures, as shown in the illustration below. The Cn3D Tutorial provides additional details about viewing structure alignments in Cn3D.
Example 3D alignment of VAST similar structures, showing the ancient evolutionary relationship among lipocalins from bacteria, insects, and human. Click on the image to open a the 3D alignment in the free Cn3D program. Please note that Cn3D must be installed in your computer in order for the file to open. .

| Revised 08 January 2015 | | Help Desk | Disclaimer | Privacy statement | Accessibility |

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