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In-Depth Information
2.2 Annotation of 3D Domains
After initial processing, 3D domains are automatically identified within each MMDB
record. 3D domains are annotations on individual MMDB structures that define the
boundaries of compact substructures contained within them. In this way, they are similar
to secondary structure annotations that define the boundaries of helical or
ȕ
-strand
substructures. Because proteins are often similar at the level of domains, VAST compares
each 3D domain to every other one and to complete polypeptide chains. The results are
stored in Entrez as a 3D Domain Neighbors link.
To identify 3D domains within a polypeptide chain, MMDB's domain parser
searches for one or more breakpoints in the structure. These breakpoints fall between
major secondary structure elements such that the ratio of intra- to interdomain contacts
remains above a set threshold. The 3D domains identified in this way provide a means to
both increase the sensitivity of structure neighbor calculations and also present 3D
superpositions based on compact domains as well as on complete polypeptide chains.
They are not intended to represent domains identified by comparative sequence and
structure analysis, nor do they represent modules that recur in related proteins, although
there is often good agreement between domain boundaries identified by these methods.
2.3 Links to Other NCBI Resources
After initially processing the PDB record, structure staff add a number of links and other
information that further integrate the MMDB record with other NCBI resources.
To begin, the sequence information extracted from the PDB record is entered into
the Entrez Protein and/or Nucleotide databases as appropriate, providing a means to
retrieve the structure information from sequence searches. As with all sequences in
Entrez, precomputed BLAST searches are then performed on these sequences, linking
them to other molecules of similar sequence. For proteins, these BLAST neighbors may
be different than those determined by VAST; whereas VAST uses a conservative
significance threshold, the structural similarities it detects often represent remote
relationships not detectable by sequence comparison. The literature citations in the PDB
record are linked to PubMed so that Entrez searches can allow access to the original
descriptions of the structure determinations. Finally, semiautomatic processing of the
“source” field of the PDB record provides links to the NCBI Taxonomy database.
Although these links normally follow the genus and species information given, in some
cases this information is either absent in the PDB record or refers only to how a sample
was obtained. In these cases, the staff manually enters the appropriate taxonomy links.
2.4 The MMDB Record
The Structure Summary page for each MMDB record summarizes the database content
for that record and serves as a starting point for analyzing the record using the NCBI
structure tools (Figure 2).
