There are several ways to retrieve similar 3D structures:
Input a PDB-formatted file directly into VAST Search
To compare the spatial coordinates of a newly resolved 3D structure against all structures in the Molecular Modeling Database (MMDB), please put your data into a text file using
PDB File format. Enter the file name in
the following line, choose the data set (all or medium redundancy) against which you want to search, and click the "Submit" button.
The (default) "Medium-redundancy Subset of PDB" is about 1/10 the size of "All
of PDB" and therefore the search will be much faster. See the VAST Search Help document for additional details about submitting a query, and the general VAST Help document for information about the output. (Please note that the results will be returned in Original VAST output format. The VAST+ output format is currently available only for structures that are publicly available in MMDB.)
Retrieve the results of a previous VAST Search
To get results of a previous job, please enter its
a number you received when submitting the previous search,
in the following line and click the "Show" button.
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;
(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:
(4) Or, 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, open the structure summary page and then either:
(a) 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 in order to view a list of other structures that are similar in shape to the specific molecule or 3D domain you selected;
(b) or follow the link for "original VAST" near the upper right corner of the VAST+ search results page.