CDD: a curated Entrez database of conserved domain alignments.
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.
Marchler-Bauer
Aron
A
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
Anderson
John B
JB
DeWeese-Scott
Carol
C
Fedorova
Natalie D
ND
Geer
Lewis Y
LY
He
Siqian
S
Hurwitz
David I
DI
Jackson
John D
JD
Jacobs
Aviva R
AR
Lanczycki
Christopher J
CJ
Liebert
Cynthia A
CA
Liu
Chunlei
C
Madej
Thomas
T
Marchler
Gabriele H
GH
Mazumder
Raja
R
Nikolskaya
Anastasia N
AN
Panchenko
Anna R
AR
Rao
Bachoti S
BS
Shoemaker
Benjamin A
BA
Simonyan
Vahan
V
Song
James S
JS
Thiessen
Paul A
PA
Vasudevan
Sona
S
Wang
Yanli
Y
Yamashita
Roxanne A
RA
Yin
Jodie J
JJ
Bryant
Stephen H
SH
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