The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

被引：195

作者：

Pearl, F

Todd, A

Sillitoe, I

Dibley, M

Redfern, O

Lewis, T

Bennett, C

Marsden, R

Grant, A

Lee, D

Akpor, A

Maibaum, M

Harrison, A

Dallman, T

Reeves, G

Diboun, I

Addou, S

Lise, S

Johnston, C

Sillero, A

Thornton, J

Orengo, C

机构：

[1] UCL, Dept Biochem & Mol Biol, London WC1E 6BT, England

[2] European Bioinformat Inst, EMBL, Cambridge CB10 1SD, England

来源：

NUCLEIC ACIDS RESEARCH | 2005年 / 33卷

基金：

英国生物技术与生命科学研究理事会; 美国国家卫生研究院; 英国惠康基金;

关键词：

D O I：

10.1093/nar/gki024

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 CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616470 domain sequences classified into 23876 sequence families. This results in the significant expansion of the CATH HMM model library to include models built from the CATH sequence relatives, giving a 10% increase in coverage for detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.uci.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.uci.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned.

引用

页码：D247 / D251

页数：5

共 19 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] The ENZYME database in 2000 [J].

Bairoch, A .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :304-305

[3]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkr1065, 10.1093/nar/gkh121]

[4] GenBank: update [J].

Benson, DA ;

Karsch-Mizrachi, I ;

Lipman, DJ ;

Ostell, J ;

Wheeler, DL .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D23-D26

[5] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[6] The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues [J].

Bray, JE ;

Todd, AE ;

Pearl, FMG ;

Thornton, JM ;

Orengo, CA .

PROTEIN ENGINEERING, 2000, 13 (03) :153-165

[7] Hidden Markov models [J].

Eddy, SR .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 1996, 6 (03) :361-365

[8] Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure [J].

Gough, J ;

Karplus, K ;

Hughey, R ;

Chothia, C .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 313 (04) :903-919

[9] The Gene Ontology (GO) database and informatics resource [J].

Harris, MA ;

Clark, J ;

Ireland, A ;

Lomax, J ;

Ashburner, M ;

Foulger, R ;

Eilbeck, K ;

Lewis, S ;

Marshall, B ;

Mungall, C ;

Richter, J ;

Rubin, GM ;

Blake, JA ;

Bult, C ;

Dolan, M ;

Drabkin, H ;

Eppig, JT ;

Hill, DP ;

Ni, L ;

Ringwald, M ;

Balakrishnan, R ;

Cherry, JM ;

Christie, KR ;

Costanzo, MC ;

Dwight, SS ;

Engel, S ;

Fisk, DG ;

Hirschman, JE ;

Hong, EL ;

Nash, RS ;

Sethuraman, A ;

Theesfeld, CL ;

Botstein, D ;

Dolinski, K ;

Feierbach, B ;

Berardini, T ;

Mundodi, S ;

Rhee, SY ;

Apweiler, R ;

Barrell, D ;

Camon, E ;

Dimmer, E ;

Lee, V ;

Chisholm, R ;

Gaudet, P ;

Kibbe, W ;

Kishore, R ;

Schwarz, EM ;

Sternberg, P ;

Gwinn, M .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D258-D261

[10] Recognizing the fold of a protein structure [J].

Harrison, A ;

Pearl, F ;

Sillitoe, I ;

Slidel, T ;

Mott, R ;

Thornton, J ;

Orengo, C .

BIOINFORMATICS, 2003, 19 (14) :1748-1759

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