Information Technology Reference
In-Depth Information
8. Links Between Structure and Other Resources
8.1 Integration with Other NCBI Resources
As illustrated in the sections above, there are numerous connections between the
Structure resources and other databases and tools available at the NCBI. What follows is
a listing of major tools that support connections.
Entrez.
Because Entrez is an integrated database system, the links attached to each
structure give immediate access to PubMed, Protein, Nucleotide, 3D Domain, CDD, or
Taxonomy records.
BLAST.
Although the BLAST service is designed to find matches based solely on
sequence, the sequences of Structure records are included in the BLAST databases, and
by selecting the PDB search database, BLAST searches only the protein sequences
provided by MMDB records. A new
Related Structure
link provides 3D views for
sequences with structure data identified in a BLAST search.
BLink.
The BLink report represents a precomputed list of similar proteins for all
sequences in Entrez Protein. The
3D Structures
option on any BLink report shows the
BLAST hits that have 3D structure data in MMDB, whereas the
CDD-Search
button
displays the CD-Search results page for the query protein.
Microbial Genomes.
A particularly useful interface with the structural databases
is provided on the Microbial Genomes page
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[10]. To the left of the list of genomes are
several hyperlinks, two of which offer users direct access to structural information. The
red
[D]
link displays a listing of every protein in the genome, each with a link to a BLink
page showing the results of a BLAST pdb search for that protein. The
[S]
link displays a
similar protein list for the selected genome, but now with a listing of the conserved
domains found in each protein by a CD-Search.
8.2 Links to Non-NCBI Resources
The Protein Data Bank (PDB).
As stated elsewhere, all records in the MMDB are
obtained originally from the Protein Data Bank (PDB) [6]. Links to the original PDB
records are located on the Structure Summary page of each MMDB record. Updates of
the MMDB with new PDB records occur once a month.
Pfam and SMART.
The CDD staff imports CD collections from both the Pfam and
SMART databases. Links to the original records in these databases are located on the
appropriate CD Summary page. Both Pfam and SMART are updated several times per
year in roughly bimonthly intervals, and the CDD staff update CDD accordingly.
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[http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/micr.html]
