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

There are several ways to retrieve similar 3D structures:
 
 
  Input a PDB-formatted file
directly into VAST Search		   The VAST Search service is a web-based tool that allows you to compare the spatial coordinates of a newly resolved 3D structure against all structures in the Molecular Modeling Database (MMDB). To use the service, place your data into a text file using PDB File format. Use the "choose file" button below to browse your computer and select the data file, and select the data set (all or medium redundancy) against which you want to search. Click the "Submit" button to begin the search. The VAST Search help document provides additional details about submitting a query. The main VAST Help document provides general information about VAST, illustrated examples of the output, and links to publications that describe the VAST algorithm.

  PDB file:
 
Searching against: Medium-redundancy Subset of PDB
  All of PDB
(Please note that the VAST Search service returns results in the Original VAST output format. The new VAST+ output format is currently available only for structures that are publicly available in MMDB. Read more about the differences between VAST and VAST+)

 
 
  Retrieve the results
of a previous VAST Search		  

To get results of a previous job, please enter its request identifier, a number you received when submitting the previous search, in the following line and click the "Show" button.

  Retrieve result by request ID:   
 
 
 
  Retrieve a 3D Structure record from MMDB → link to similar structures   If your structure of interest is already available in the Molecular Modeling Database (MMDB), a VAST search has been conducted and the precalculated VAST, and VAST+, results are accessible from the structure's summary page. To view the precalculated results:

(1) Retrieve a structure record of interest by PDB ID, MMDB ID, or text term.

(2) Open its structure summary page.

(3) Click on the "Similar Structures: VAST+" link near the upper right corner of the summary page. That will open the new VAST+ search results page, which lists the query structure followed by similar structures, ranked by the degree of similarity to the query structure's biological unit.

As a shortcut to the VAST+ results for your structure of interest, simply enter its PDB ID or MMDB ID in the form below:

Show Similar Structures for:

If you prefer to see the original VAST results, which focus on similarities between individual protein molecules or 3D domains within the query structure and hits, then click on the "Original VAST" button near the upper right corner of the VAST+ search results page.
Alternatively, you can access original VAST results for individual proteins within your query structure by following these steps: open the query structure's summary page; scroll down to the table of molecules and interactions; 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. That will display a list of other structures that are similar in shape to the specific molecule or 3D domain you selected;

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.
 
 
 
Revised 26 September 2016