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VAST: Vector Alignment Search Tool
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, short for V
ool, 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.
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:
1. view the " show annotation
" graphic for any protein molecule of interest on a structure summary page, 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.
2. follow the link for " Similar Structures: VAST
" in the upper right corner of a structure summary page to open a tabular list of the protein molecules and 3D domains
in the structure. Then select the protein or 3D domain of interest to view a list of structures that are similar in shape to the region you selected.
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.
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.
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