VAST: Vector Alignment Search Tool
ABOUT SEARCH HELP nr-PDB PUBLICATIONS RESOURCES NEWS DISCOVER
, short for V
ool, 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 3D similar to individual protein molecules
, or individual 3D domains
. The original-style VAST display can be viewed by clicking on the "Original VAST" button
on any VAST+ search results page. The original VAST help document
provides an illustrated examples
of original style VAST search results
, alignment footprints
, and an example 3D superposition
of lipocalins from bacteria, insect, and human. The VAST+ help document
provides illustrated examples of the newer VAST+ search results
, where you can see the "Original VAST" button near the upper right corner of each illustration, and summarizes the difference between VAST and VAST+
provide additional details about both.
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
, finds structures that are 3D similar to your query structure's macromolecular complex
( biological unit
). 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. The VAST+ help document
provides illustrated examples of VAST+ search results
, featuring similar structures for glutamate dehydrogenase
) and deoxyhemoglobin
). The help document also describes 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."
The new style VAST+ results
are displayed by default. Illustrated examples of VAST + search results
are available in VAST+ help document
and in the thumbnail to the right.
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, you can use the VAST Search
service to input
your data in PDB file format
and compare your structure against all those in MMDB in order to find 3D similar structures. 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 17 March 2015