3D Macromolecular Structures
How to compare a newly resolved 3D structure in PDB format against the 3D coordinates of structures in MMDB

If you have the 3D coordinates of a structure in PDB format, you can use the VAST Search tool to compare your structure against those in the Entrez Structure database (also known as the Molecular Modeling Database, "MMDB") in order to find similar 3D structures:

  • Upload your PDB format structure file into the VAST Search tool.

  • VAST Search results will parse your data file and present a summary of the protein chains and 3D domains present in your structure (illustrated example). At this point, you can use the View 3D Structure button to interactively view your structure and the corresponding sequence data in the Cn3D program, or the Start button to begin the VAST calculation.

  • If you press the Start button, the VAST search results page will list the 3D structures that are geometrically similar to all or part of each protein chain in your query structure (illustrated example). 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 "medium redundancy" 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 selected structures 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.)

Revised 17 March 2015