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), a graphical display at the bottom of the page will show the 3D domains that have been identified in each protein chain of the query structure. Click on a 3D domain of interest to view a list of structures that are geometrically similar to that domain, as identified by VAST.



• The List options at the top of the VAST Search results page 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. Cn3D can display up to 10 superposed structures. (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."