title: CDD: a curated Entrez database of conserved domain alignments.
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.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA. bauer@ncbi.nlm.nih.gov
authors.forename: Aron
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authors.lastname: Marchler-Bauer
authors.forename: John B
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authors.lastname: Anderson
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authors.lastname: DeWeese-Scott
authors.forename: Natalie D
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authors.lastname: Fedorova
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authors.forename: David I
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authors.lastname: Hurwitz
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authors.initials: JD
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authors.forename: Aviva R
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authors.lastname: Jacobs
authors.forename: Christopher J
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authors.lastname: Lanczycki
authors.forename: Cynthia A
authors.initials: CA
authors.lastname: Liebert
authors.forename: Chunlei
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authors.lastname: Liu
authors.forename: Thomas
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authors.lastname: Madej
authors.forename: Gabriele H
authors.initials: GH
authors.lastname: Marchler
authors.forename: Raja
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authors.lastname: Mazumder
authors.forename: Anastasia N
authors.initials: AN
authors.lastname: Nikolskaya
authors.forename: Anna R
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authors.lastname: Panchenko
authors.forename: Bachoti S
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authors.lastname: Rao
authors.forename: Benjamin A
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authors.lastname: Shoemaker
authors.forename: Vahan
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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: Sona
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authors.lastname: Vasudevan
authors.forename: Yanli
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authors.lastname: Wang
authors.forename: Roxanne A
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authors.lastname: Yamashita
authors.forename: Jodie J
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authors.lastname: Yin
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authors.lastname: Bryant
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017124:Conserved Sequence; D030562:Databases, Protein; D016247:Information Storage and Retrieval; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment