title: CDD: a conserved domain database for interactive domain family analysis.
abstract: 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. Entrez's global query interface can be accessed at http://www.ncbi.nlm.nih.gov/Entrez and will search CDD and many other databases. Domain annotation for proteins in Entrez has been pre-computed and is readily available in the form of 'Conserved Domain' links. Novel protein sequences can be scanned against CDD using the CD-Search service; this service searches databases of CDD-derived profile models with protein sequence queries using BLAST heuristics, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. The CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at NCBI. NCBI curated models are organized into hierarchies of domains related by common descent. Here we report on the status of the curation effort and present a novel helper application, CDTree, which enables users of the CDD resource to examine curated hierarchies. More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.
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: Myra K
authors.initials: MK
authors.lastname: Derbyshire
authors.forename: Carol
authors.initials: C
authors.lastname: DeWeese-Scott
authors.forename: Noreen R
authors.initials: NR
authors.lastname: Gonzales
authors.forename: Marc
authors.initials: M
authors.lastname: Gwadz
authors.forename: Luning
authors.initials: L
authors.lastname: Hao
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: Dmitri
authors.initials: D
authors.lastname: Krylov
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: Shennan
authors.initials: S
authors.lastname: Lu
authors.forename: Gabriele H
authors.initials: GH
authors.lastname: Marchler
authors.forename: Mikhail
authors.initials: M
authors.lastname: Mullokandov
authors.forename: James S
authors.initials: JS
authors.lastname: Song
authors.forename: Narmada
authors.initials: N
authors.lastname: Thanki
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; D000818:Animals; D017124:Conserved Sequence; D030562:Databases, Protein; D020407:Internet; D010802:Phylogeny; D017434:Protein Structure, Tertiary / Q000235:genetics; D011506:Proteins / Q000145:classification; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
chemical_list: D011506:Proteins