3D Macromolecular Structures
 
 
 
 
How to find structures with similarly shaped biological assemblies, regardless of their degree of sequence similarity
 
 

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 other structures that have similarly shaped proteins or 3D domains (substructures), based on purely geometrical criteria. These may represent distant homologs that cannot be recognized by sequence comparison alone.

An additional tool, called, VAST+, is built upon the original VAST and expands the capabilities of that program by making it possible to now find macromolecular structures that have similarly shaped biological assemblies ("biological units," or "biounits"), not just those that share similarly shaped individual protein molecules or substructures.


If your structure of interest is already available in the Entrez Structure (MMDB) database:

  • The VAST+ results page will display summary information about your query structure, followed by a ranked list of structures that are similar in 3D shape to the query structure you specified, with an emphasis on those that have a biological unit similar to the query.


  • Click on the plus button The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit. beside any structure to see a detailed view/graphical display comparing that structure to your query. The display includes side-by-side interaction schematics that compare the composition and configuraton of the structures' biological assemblies, a table that lists the names of matching proteins in the query structure and subject, and 3D View" button beside each pair of matched protein molecules, which opens a superposition of the complete biological unit alignment, with the 3D view centered on the selected protein molecule and its sequence data featured in the Cn3Dís sequence alignment window. (You must install the most recent version of the NCBI molecular viewing software, Cn3D 4.3.1. 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 you would like to find structures that have similarly shaped individual proteins or 3D domains to your query structure, rather than similarly shaped biological assemblies, then follow the steps in "How to find structures with similarly shaped proteins or 3D domains, regardless of their degree of sequence similarity. [VAST]."



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."

 
 
 
Revised 23 September 2016