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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 by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison.

This page reflects the Original VAST resource, which finds other protein structures that contain one or more similarly shaped proteins or 3D domains. An enhanced resource, VAST+, is also available, and finds structures with similar macromolecular complexes.

VAST is applied on every protein in the Molecular Modeling Database (MMDB) during MMDB data processing in order to identify similar 3D structures. The pre-computed results are accessible from a structure's summary page; to retrieve them, you can either:

• Retrieve a structure of interest from MMDB and open its structure summary page. Follow the "Similar Structures: VAST+" link near the upper right corner of a structure's MMDB structure summary page. That will open the new VAST+ search results page ( illustrated example), which lists the query structure followed by similar structures, ranked by the degree of similarity to the query structure's biological unit. If you prefer to see the original style VAST results, which focus on similarities between individual protein molecules or 3D domains within the query structure and hits, follow the link for " original VAST" near the upper right corner of the VAST+ search results page. The VAST+ help document provides details about the differences between VAST and VAST+, an illustrated example of VAST+ results, and an illustrated example of original VAST results.
Show "Similar Structures: VAST+" for PDB ID or MMDB ID:
• Retrieve a structure of interest from MMDB and open its structure summary page. View the " show annotation" graphic for any protein molecule of interest, then click on the bar graphic for the overall protein molecule or for any 3D domain it contains in order to view a list of structures that are similar in shape to the molecule or 3D domain you selected. The VAST Help document provides additional details and illustrated examples.

If you have a newly determined 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 VAST format, 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.)

Whether you retrieve similar structures from the summary page of a publicly available structure or through a 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 16 December 2013 | | Help Desk | Disclaimer | Privacy statement | Accessibility |

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