title: CDD: a Conserved Domain Database for protein classification.
abstract: The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein-protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.
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: John B
authors.initials: JB
authors.lastname: Anderson
authors.forename: Praveen F
authors.initials: PF
authors.lastname: Cherukuri
authors.forename: Carol
authors.initials: C
authors.lastname: DeWeese-Scott
authors.forename: Lewis Y
authors.initials: LY
authors.lastname: Geer
authors.forename: Marc
authors.initials: M
authors.lastname: Gwadz
authors.forename: Siqian
authors.initials: S
authors.lastname: He
authors.forename: David I
authors.initials: DI
authors.lastname: Hurwitz
authors.forename: John D
authors.initials: JD
authors.lastname: Jackson
authors.forename: Zhaoxi
authors.initials: Z
authors.lastname: Ke
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Lanczycki
authors.forename: Cynthia A
authors.initials: CA
authors.lastname: Liebert
authors.forename: Chunlei
authors.initials: C
authors.lastname: Liu
authors.forename: Fu
authors.initials: F
authors.lastname: Lu
authors.forename: Gabriele H
authors.initials: GH
authors.lastname: Marchler
authors.forename: Mikhail
authors.initials: M
authors.lastname: Mullokandov
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Shoemaker
authors.forename: Vahan
authors.initials: V
authors.lastname: Simonyan
authors.forename: James S
authors.initials: JS
authors.lastname: Song
authors.forename: Paul A
authors.initials: PA
authors.lastname: Thiessen
authors.forename: Roxanne A
authors.initials: RA
authors.lastname: Yamashita
authors.forename: Jodie J
authors.initials: JJ
authors.lastname: Yin
authors.forename: Dachuan
authors.initials: D
authors.lastname: Zhang
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Bryant
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D030562:Databases, Protein; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000145:classification*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
chemical_list: D011506:Proteins