Information Technology Reference
In-Depth Information
to each MMDB entry. For those who have a set of 3D coordinates for a protein not yet in
MMDB, there is also a VAST search service
5
.
Figure 1: The Structure homepage.
This page can be found by selecting the
Structure
link on the tool bar
atop many NCBI Web pages. Two searches can be performed from this page, an
Entrez Structure
search or
a
Structure Summary
search. Both query the MMDB database. The difference is that Entrez Structure can
take any text as a query (such as a PDB code, protein name, text word, author, or journal) and will result
initially in a list of one or more document summaries, displayed within the Entrez environment, whereas
only a PDB code or MMDB ID number can be used for the Structure Summary search, resulting in direct
display of the Structure Summary page for that record (Figure 2). Announcements about new features or
updates can also be found on this page, as well as links to more specialized pages on the various Structure
databases and tools.
The output of the precomputed VAST searches is a list of structure records, each
representing one of the Non-Redundant PDB chain sets (nr-PDB)
6
, which can also be
downloaded. There are four clustered subsets of MMDB that compose nr-PDB, each
consisting of clusters having a preset level of sequence similarity.
5
[http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml]
6
http://www.ncbi.nlm.nih.gov/Structure/VAST/nrpdb.html
