title: CDD: a database of conserved domain alignments with links to domain three-dimensional structure.
abstract: 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 and SMART, as well as with contributions from colleagues at NCBI. The current version of CDD (v.1.54) contains 3693 such models. CDD alignments are linked to protein sequence and structure data in Entrez. The molecular structure viewer Cn3D serves as a tool to interactively visualize alignments and three-dimensional structure, and to link three-dimensional residue coordinates to descriptions of evolutionary conservation. CDD can be accessed on the World Wide Web at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. Protein query sequences may be compared against databases of position-specific score matrices derived from alignments in CDD, using a service named CD-Search, which can be found at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search runs reverse-position-specific BLAST (RPS-BLAST), a variant of the widely used PSI-BLAST algorithm. CD-Search is run by default for protein-protein queries submitted to NCBI's BLAST service at http://www.ncbi.nlm.nih.gov/BLAST.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA. bauer@ncbi.nlm.nih.gov
authors.forename: Aron
authors.initials: A
authors.lastname: Marchler-Bauer
authors.forename: Anna R
authors.initials: AR
authors.lastname: Panchenko
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Shoemaker
authors.forename: Paul A
authors.initials: PA
authors.lastname: Thiessen
authors.forename: Lewis Y
authors.initials: LY
authors.lastname: Geer
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Bryant
mesh_terms: D000818:Animals; D003196:Computer Graphics; D017124:Conserved Sequence; D030562:Databases, Protein; D005544:Forecasting; D021621:Imaging, Three-Dimensional; D016247:Information Storage and Retrieval; D020407:Internet; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D011506:Proteins