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.
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 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 search results are accessible from the structure's summary page. To view the VAST search results:
(1) retrieve a structure record of interest by PDB ID, MMDB ID, or text term;
(2) open its structure summary page; then either:
(3) view the "show annotation" graphic for any protein molecule of interest; and 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 molecule or 3D domain you selected. OR:
(4) click on the "Similar Structures: VAST" link near the upper right corner of the summary page. That will open a dialog box listing the individual protein molecules that compose the structure, and the 3D domains detected in each one. Select a protein molecule or 3D domain of interest to view a list of other structures that are similar in shape to the molecule or 3D domain you selected. As a shortcut to this particular view, you can use the form below:
