MMDB is an integrated part of Entrez and can be accessed by querying Entrez’s ‘structure’ database for particular terms or keywords. This allows one to identify structures based on protein names, for example, or author names, publication dates or species names. A simple boolean query will produce a list of MMDB entries. One may browse this list, following links to other databases, for example those to Medline® abstracts.
The latest version of Entrez supports a powerful query refinement feature, allowing one to logically combine the results of simple queries involving term-match hits, links or neighbors. Suppose, for example, one wishes to select from among the structure neighbors of a protein those that are also sequence neighbors. One query may select structure neighbors of the protein. Another may in turn select the protein’s sequence link, its sequence neighbors and those neighbors’ structure links. Since Entrez stores query results in its ‘history’, one may now combine the simple queries by asking for ‘<q1> AND <q2>’, where <q1> and <q2> represent selections from Entrez’s ‘history’.
Selecting the ‘Structure Summary’ for an MMDB entry, one finds a detailed choice of links and visualization options. The default ‘View’ will launch NCBI’s Cn3D molecular graphics viewer. One may also choose links to ‘Structure Neighbors’ of individual chains and/or domains. This leads to a detailed listing of VAST neighbor results, with ‘View’ options to display structure–structure superpositions, and numerical scores describing the extent of structural similarity. Using Cn3D one may view the corresponding sequence alignments in intercommunicating windows. For more information and downloading instructions for Cn3D, see: http://www.ncbi. nlm.nih.gov/Structure/CN3D
As a service to structural biologists, NCBI supports ‘on the fly’ structure neighbor calculation. Users may submit coordinates for a new structure or domain, and when the search is complete, browse a neighbor list of the same form as available in Entrez. VAST-Search results are accessible only to the user requesting the search. For further information see: http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html
A large portion of the protein sequences in complete genomes share significant sequence similarities with proteins of known 3D structure. As a service to genome annotators, we have linked these protein sequences to BLAST sequence neighbors in MMDB. The new service lists sequence neighbors with links to structure, and allows users to view the corresponding sequence–structure alignments. See the ‘PDB neighbors’ for genomes listed in: http://www.ncbi.nlm.nih.gov/Entrez/Genome/ org.html