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. 2003 Jan 1;31(1):383-7.
doi: 10.1093/nar/gkg087.

CDD: a curated Entrez database of conserved domain alignments

Affiliations

CDD: a curated Entrez database of conserved domain alignments

Aron Marchler-Bauer et al. Nucleic Acids Res. .

Abstract

The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R). This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. CDD can be accessed on the WorldWideWeb at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein-protein queries submitted to BLAST(R) at http://www.ncbi.nlm.nih.gov/BLAST. CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members.

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Figures

Figure 1
Figure 1
Pre-calculated CD-Search results are readily available for protein sequences in Entrez. Clicking on the coloured bars will launch alignment displays that merge the query into the domain alignment model, for further analysis. Domain annotation bars with identical colours have been grouped into sets of ‘related’ domains, indicating that they share many of the sequence intervals hit with significant E-values.
Figure 2
Figure 2
Visualization of ‘structure evidence’ for a feature recorded in CDD. The feature shown here is the nucleotide-binding pocket in cd00114 or LIGANc, the NAD-dependent subgroup of DNA ligases. The default colour scheme used by the WWW-server is green for residues, which are part of the feature evidence, and orange for heterogen groups.

References

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