CDD: a conserved domain database for interactive domain family analysis

被引：675

作者：

Marchler-Bauer, Aron ^{[1
]}

Anderson, John B. ^{[1
]}

Derbyshire, Myra K. ^{[1
]}

DeWeese-Scott, Carol ^{[1
]}

Gonzales, Noreen R. ^{[1
]}

Gwadz, Marc ^{[1
]}

Hao, Luning ^{[1
]}

He, Siqian ^{[1
]}

Hurwitz, David I. ^{[1
]}

Jackson, John D. ^{[1
]}

Ke, Zhaoxi ^{[1
]}

Krylov, Dmitri ^{[1
]}

Lanczycki, Christopher J. ^{[1
]}

Liebert, Cynthia A. ^{[1
]}

Liu, Chunlei ^{[1
]}

Lu, Fu ^{[1
]}

Lu, Shennan ^{[1
]}

Marchler, Gabriele H. ^{[1
]}

Mullokandov, Mikhail ^{[1
]}

Song, James S. ^{[1
]}

Thanki, Narmada ^{[1
]}

Yamashita, Roxanne A. ^{[1
]}

Yin, Jodie J. ^{[1
]}

Zhang, Dachuan ^{[1
]}

Bryant, Stephen H. ^{[1
]}

机构：

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

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/nar/gkl951

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 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.

引用

页码：D237 / D240

页数：4

共 10 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] Functional classification using phylogenomic inference [J].

Brown, Duncan ;

Sjolander, Kimmen .

PLOS COMPUTATIONAL BIOLOGY, 2006, 2 (06) :479-483

[3] Pfam:: clans, web tools and services [J].

Finn, Robert D. ;

Mistry, Jaina ;

Schuster-Bockler, Benjamin ;

Griffiths-Jones, Sam ;

Hollich, Volker ;

Lassmann, Timo ;

Moxon, Simon ;

Marshall, Mhairi ;

Khanna, Ajay ;

Durbin, Richard ;

Eddy, Sean R. ;

Sonnhammer, Erik L. L. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D247-D251

[4] CDART: Protein homology by domain architecture [J].

Geer, LY ;

Domrachev, M ;

Lipman, DJ ;

Bryant, SH .

GENOME RESEARCH, 2002, 12 (10) :1619-1623

[5] SMART 5: domains in the context of genomes and networks [J].

Letunic, Ivica ;

Copley, Richard R. ;

Pils, Birgit ;

Pinkert, Stefan ;

Schultz, Joerg ;

Bork, Peer .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D257-D260

[6] CDD: a conserved domain database for protein classification [J].

Marchler-Bauer, A ;

Anderson, JB ;

Cherukuri, PF ;

DeWweese-Scott, C ;

Geer, LY ;

Gwadz, M ;

He, SQ ;

Hurwitz, DI ;

Jackson, JD ;

Ke, ZX ;

Lanczycki, CJ ;

Liebert, CA ;

Liu, CL ;

Lu, F ;

Marchler, GH ;

Mullokandov, M ;

Shoemaker, BA ;

Simonyan, V ;

Song, JS ;

Thiessen, PA ;

Yamashita, RA ;

Yin, JJ ;

Zhang, DC ;

Bryant, SH .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D192-D196

[7] CD-Search: protein domain annotations on the fly [J].

Marchler-Bauer, A ;

Bryant, SH .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W327-W331

[8] The COG database: an updated version includes eukaryotes [J].

Tatusov, RL ;

Fedorova, ND ;

Jackson, JD ;

Jacobs, AR ;

Kiryutin, B ;

Koonin, EV ;

Krylov, DM ;

Mazumder, R ;

Mekhedov, SL ;

Nikolskaya, AN ;

Rao, BS ;

Smirnov, S ;

Sverdlov, AV ;

Vasudevan, S ;

Wolf, YI ;

Yin, JJ ;

Natale, DA .

BMC BIOINFORMATICS, 2003, 4 (1)

[9] Cn3D: sequence and structure views for Entrez [J].

Wang, YL ;

Geer, LY ;

Chappey, C ;

Kans, JA ;

Bryant, SH .

TRENDS IN BIOCHEMICAL SCIENCES, 2000, 25 (06) :300-302

[10] Database resources of the national center for biotechnology information [J].

Wheeler, David L. ;

Barrett, Tanya ;

Benson, Dennis A. ;

Bryant, Stephen H. ;

Canese, Kathi ;

Chetvernin, Vyacheslav ;

Church, Deanna M. ;

DiCuccio, Michael ;

Edgar, Ron ;

Federhen, Scott ;

Geer, Lewis Y. ;

Helmberg, Wolfgang ;

Kapustin, Yuri ;

Kenton, David L. ;

Khovayko, Oleg ;

Lipman, David J. ;

Madden, Thomas L. ;

Maglott, Donna R. ;

Ostell, James ;

Pruitt, Kim D. ;

Schuler, Gregory D. ;

Schriml, Lynn M. ;

Sequeira, Edwin ;

Sherry, Stephen T. ;

Sirotkin, Karl ;

Souvorov, Alexandre ;

Starchenko, Grigory ;

Suzek, Tugba O. ;

Tatusov, Roman ;

Tatusova, Tatiana A. ;

Wagner, Lukas ;

Yaschenko, Eugene .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D173-D180

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