VAST: Vector Alignment Search Tool
ABOUT SEARCH   VAST HELP   nr-PDB   PUBLICATIONS   RESOURCES   NEWS   DISCOVER  

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
individual protein molecules
or 3D domains   Example 3D alignment of VAST similar structures, showing the ancient evolutionary relationship among lipocalins from bacteria, insects, and human. Click on the image to view the enlarged, annotated version at the bottom of this page.
The original VAST finds structures that are similar to individual protein molecules, or individual 3D domains, in your query structure, as shown in the thumbnail to the right (superposition of lipocalins from bacteria, insect, and human). Click on the thumbnail to view the enlarged and annotated illustrated example in the original VAST help document. The original-style VAST display can be viewed by clicking on the "Original VAST" button on any VAST+ search results page. (By default, similar structures are displayed in the new VAST+ style, including for searches entered in the " Retrieve pre-computed results" section of this page, and the original VAST results are just one click away.) Read more about the difference between VAST and VAST+.

Find similarly shaped
macromolecular complexes   Example VAST+ similar structures, showing the interaction schematics of glutamate dehydrogenase molecular complexes from Thermotoga maritima and Pyrococcus furiosus. Click on the image to view the enlarged, annotated version in the VAST+ help document.
An enhanced resource, VAST+, is also available, and finds structures that are similar to your query structure's macromolecular complex ( biological unit), as shown in the thumbnail to the right (glutamate dehydrogenase from Thermotoga maritima and Pyrococcus furiosus). Click on the thumbnail to view the enlarged and annotated illustrated example in the VAST+ help document, where you can also read about the difference between VAST and VAST+. The search form in the " Retrieve pre-computed results" section of this page, below, will retrieve VAST+ results for the query structure that you specify.

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 displayed by default, as shown in the thumbnail to the right (for human deoxyhemoglobin, PDB ID: 1HBB). Click on the thumbnail to view the enlarged and annotated illustrated example in the VAST+ help document.

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+.   Example VAST+ similar structures, showing an excerpt of the search results for human deoxyhemoglobin (1HBB). Click on the image to view the enlarged, annotated version in the VAST+ help document.

Search with a new structure
(PDB formatted file)   Schematic image depicting the upload of a newly resolved structure in PDB file format to VAST Search, which finds similarly shaped 3D structures and displays their alignment footprints, with options to view sequence alignments and 3D superpositions. Click on the image to open the VAST Search page.
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, which lists structures that have similarities to individual protein molecules and 3D domains in your query structure, and allows you to view their sequence alignments and 3D superpositions. The new VAST+ search results, which rank similar structures based on their biological unit similarity to the query structure, and provide the ability to view sequence alignments and superpositions of the biological units, are currently calculated only for structures that are available in the public database.
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 illustrated example of lipocalins from bacteria, insects, and human that appears in the original VAST help document. Click on that illustration to open the interactive 3D alignment in the free Cn3D program. Please note that Cn3D 4.3.1 must be installed in your computer in order for the file to open. The Cn3D Tutorial provides additional details about viewing structure alignments in Cn3D.

Revised 12 February 2015
Text Only Options

Top of page


Text Only Options

Open the original version of this page.

Usablenet Assistive is a UsableNet product. Usablenet Assistive Main Page.