Gene3D: modelling protein structure, function and evolution

被引：34

作者：

Yeats, Corin ^{[1
]}

Maibaum, Michael ^{[1
]}

Marsden, Russell ^{[1
]}

Dibley, Mark ^{[1
]}

Lee, David ^{[1
]}

Addou, Sarah ^{[1
]}

Orengo, Christine A. ^{[1
]}

机构：

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

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷

关键词：

D O I：

10.1093/nar/gkj057

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 Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives-including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository formanually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein-protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

引用

页码：D281 / D284

页数：4

共 24 条

[1] The Biomolecular Interaction Network Database and related tools 2005 update [J].

Alfarano, C ;

Andrade, CE ;

Anthony, K ;

Bahroos, N ;

Bajec, M ;

Bantoft, K ;

Betel, D ;

Bobechko, B ;

Boutilier, K ;

Burgess, E ;

Buzadzija, K ;

Cavero, R ;

D'Abreo, C ;

Donaldson, I ;

Dorairajoo, D ;

Dumontier, MJ ;

Dumontier, MR ;

Earles, V ;

Farrall, R ;

Feldman, H ;

Garderman, E ;

Gong, Y ;

Gonzaga, R ;

Grytsan, V ;

Gryz, E ;

Gu, V ;

Haldorsen, E ;

Halupa, A ;

Haw, R ;

Hrvojic, A ;

Hurrell, L ;

Isserlin, R ;

Jack, F ;

Juma, F ;

Khan, A ;

Kon, T ;

Konopinsky, S ;

Le, V ;

Lee, E ;

Ling, S ;

Magidin, M ;

Moniakis, J ;

Montojo, J ;

Moore, S ;

Muskat, B ;

Ng, I ;

Paraiso, JP ;

Parker, B ;

Pintilie, G ;

Pirone, R .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D418-D424

[2] 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

[3] SCOP database in 2004: refinements integrate structure and sequence family data [J].

Andreeva, A ;

Howorth, D ;

Brenner, SE ;

Hubbard, TJP ;

Chothia, C ;

Murzin, AG .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D226-D229

[4] The universal protein resource (UniProt) [J].

Bairoch, Amos ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Puy, Ghislaine Argoud ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

deCastro, Edouard ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

Dobrokhotov, Pavel ;

Dornevil, Dolnide ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Feuermann, Marc ;

Gehant, Sebastian ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

Ioannidis, Vassilios ;

Ivanyi, Ivan ;

James, Janet ;

Jain, Eric ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra ;

Lara, Vicente ;

Lemercier, Philippe ;

Le Saux, Virginie .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D193-D197

[5]

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

[6] The Distributed Annotation System [J].

Dowell, Robin D. ;

Jokerst, Rodney M. ;

Day, Allen ;

Eddy, Sean R. ;

Stein, Lincoln .

BMC BIOINFORMATICS, 2001, 2 (1)

[7] MUSCLE: multiple sequence alignment with high accuracy and high throughput [J].

Edgar, RC .

NUCLEIC ACIDS RESEARCH, 2004, 32 (05) :1792-1797

[8] Multi-domain proteins in the three kingdoms of life:: Orphan domains and other unassigned regions [J].

Ekman, D ;

Björklund, ÅK ;

Frey-Skött, J ;

Elofsson, A .

JOURNAL OF MOLECULAR BIOLOGY, 2005, 348 (01) :231-243

[9] An efficient algorithm for large-scale detection of protein families [J].

Enright, AJ ;

Van Dongen, S ;

Ouzounis, CA .

NUCLEIC ACIDS RESEARCH, 2002, 30 (07) :1575-1584

[10] 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

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