CDD: a curated Entrez database of conserved domain alignments

被引：644

作者：

Marchler-Bauer, A ^{[1
]}

Anderson, JB ^{[1
]}

DeWeese-Scott, C ^{[1
]}

Fedorova, ND ^{[1
]}

Geer, LY ^{[1
]}

He, SQ ^{[1
]}

Hurwitz, DI ^{[1
]}

Jackson, JD ^{[1
]}

Jacobs, AR ^{[1
]}

Lanczycki, CJ ^{[1
]}

Liebert, CA ^{[1
]}

Liu, CL ^{[1
]}

Madej, T ^{[1
]}

Marchler, GH ^{[1
]}

Mazumder, R ^{[1
]}

Nikolskaya, AN ^{[1
]}

Panchenko, AR ^{[1
]}

Rao, BS ^{[1
]}

Shoemaker, BA ^{[1
]}

Simonyan, V ^{[1
]}

Song, JS ^{[1
]}

Thiessen, PA ^{[1
]}

Vasudevan, S ^{[1
]}

Wang, YL ^{[1
]}

Yamashita, RA ^{[1
]}

Yin, JJ ^{[1
]}

Bryant, SH ^{[1
]}

机构：

[1] Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD 20894 USA

来源：

NUCLEIC ACIDS RESEARCH | 2003年 / 31卷 / 01期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/nar/gkg087

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 WorldWide Web 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 1 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.

引用

页码：383 / 387

页数：5

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