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biointelligence
11th jan 2010
CDD: Database for Interactive Domain Family Analysis
Protein domains may be viewed as units in the molecular evolution of
proteins and can be organized into an evolutionary classification. The set
of protein domains characterized so far appears to describe no more than a
few thousand superfamilies, where members of each superfamily are related to
each other by common descent. Computational annotation of protein function
is generally obtained via sequence similarity: once a close neighbor with
known function has been identified, its annotation is copied to the sequence
with unknown function. This strategy may work very well in functionally
homogeneous families and when applied only for very close neighbors or
suspected orthologs, but it is doomed to fail often when domain or protein
families are sufficiently diverse and when no close neighbors with known
function are available.
NCBI's conserved domain
database (CDD) attempts to collate that set and to organize related domain
models in a hierarchical fashion, meant to reflect major ancient gene
duplication events and subsequent functional diversification. The conserved
domain database (CDD) is part of NCBI's Entrez database system and serves as
a primary resource for the annotation of conserved domain footprints on
protein sequences in Entrez.CDD provides a strategy toward a more accurate
assessment of such neighbor relationships, similar to approaches termed
‘phylogenomic inference. CDD acknowledges that protein domain families may
be very diverse and that they may contain sets of related subfamilies.
In CDD curation, we
attempt to detect evidence for duplication and functional divergence in
domain families by means of phylogenetic analysis. We record the resulting
subfamily structure as a set of explicit models, but limit the analysis to
ancient duplication events—several hundred million years in the past, as
judged by the taxonomic distribution of protein sequences with particular
domain subfamily footprints. CDD provides a search tool employing reverse
position-specific BLAST (RPS–BLAST), where query sequences are compared to
databases of position-specific score matrices (PSSMs), and E-values are
obtained in much the same way as in the widely used PSI-BLAST application.
CDD is hosted here: http://www.ncbi.nlm.nih.gov/Structure/cdd/cd
Regards,
Team Biointelligence
Biointelligence
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