CDD: a Conserved Domain Database for protein classification.
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.
Marchler-Bauer
Aron
A
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
Anderson
John B
JB
Cherukuri
Praveen F
PF
DeWeese-Scott
Carol
C
Geer
Lewis Y
LY
Gwadz
Marc
M
He
Siqian
S
Hurwitz
David I
DI
Jackson
John D
JD
Ke
Zhaoxi
Z
Lanczycki
Christopher J
CJ
Liebert
Cynthia A
CA
Liu
Chunlei
C
Lu
Fu
F
Marchler
Gabriele H
GH
Mullokandov
Mikhail
M
Shoemaker
Benjamin A
BA
Simonyan
Vahan
V
Song
James S
JS
Thiessen
Paul A
PA
Yamashita
Roxanne A
RA
Yin
Jodie J
JJ
Zhang
Dachuan
D
Bryant
Stephen H
SH
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
D011506:Proteins