Also known as:
- Conserved Domain Database at NCBI
Conserved Domain Database
Facts from the Community
From the Bio2RDF Semantic knowledge map base
Reserved namespace:
- cdd
Description:
- The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domains conserved in molecular evolution. It has been populated with alignment data from the public collections Pfam ( 1) and Smart ( 2), as well as with contributions from colleagues at NCBI. The current version of CDD (v1.53) contains 3551 such models. CDD alignments are linked to protein sequence and structure data in Entrez (3 ). The molecular structure viewer Cn3D (4 ) serves as a tool to interactively visualize alignments and three-dimensional structure, and to annotate three-dimensional residue coordinates with evolutionarily conserved features. CDD can be accessed on the world-wide-web at the URL a href=http:www.ncbi.nlm.nih.govStructurecddcdd.shtmlhttp:www.ncbi.nlm.nih.govStructurecddcdd.shtmla. Protein query sequences may be compared against databases of position-specific score matrices (PSSMs) derived from alignments in CDD, using a service named CD-Search, which can be found at a href=http:www.ncbi.nlm.nih.govStructurecddwrpsb.cgihttp:www.ncbi.nlm.nih.govStructurecddwrpsb.cgia. CD-Search runs reverse position-specific BLAST (RPS-BLAST), a variant of the widely used PSI-BLAST algorithm ( 5). CD-Search is run by default for protein-protein queries submitted to NCBI's BLAST-service at a href=http:www.ncbi.nlm.nih.govBLASThttp:www.ncbi.nlm.nih.govBLASTa.
Provider homepage:
- http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
Identifier example:
- pfam01484
URL pattern:
- http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s
