As part of the data processing procedures at NCBI, all protein 3D structures in the Molecular Modeling Database (MMDB) have been compared against each other using the Vector Alignment Search Tool (VAST) in order to identify geometrically similar structures. These may represent distant homologs that cannot be recognized by sequence comparison alone. There are two ways to find similar structures:
If your structure of interest is already available in the Entrez Structure (MMDB) database:
- Simply retrieve a structure of interest from the Entrez Structure (MMDB) database.
- Once you are viewing the structure's summary page (for example, 1PTH), you can do either of the following:
- 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.
- Scroll down to the table of "Molecules and interactions." 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.
- The the VAST Search results page provides various "List" options, which allow you to control the number of VAST hits you see. Because the number of hits can be large, only a subset of hits is shown by default; you can change the List option to view All Sequences, if desired.
- Use the check boxes to select hits of interest and press the View 3D Alignment button to view your structure superposed onto the geometrically similar structure in Cn3D, along with a corresponding sequence alignment (illustrated example). (In order for the "View 3D Alignment" button to work, the Cn3D program must be present on your computer. It is a free helper application available for Windows, Macintosh, and Unix platforms. Installation takes only a couple of minutes and a tutorial describes the program's features and functions.)
If your structure of interest is not yet available in the Entrez Structure (MMDB) database, then follow the steps in "How to compare a newly resolved 3D structure in PDB format against the 3D coordinates of structures in MMDB."