PROCOGNATE: a cognate ligand domain mapping for enzymes

被引：34

作者：

Bashton, Matthew ^{[1
]}

Nobeli, Irene ^{[2
]}

Thornton, Janet M. ^{[1
]}

机构：

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

[2] Kings Coll London, Randall Div Cell & Mol Biophys, London SE1 1UL, England

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkm611

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：

PROCOGNATE is a database of protein cognate ligands for the domains in enzyme structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a flat file. This article gives an overview of the database and its generation and presents a new website front end, as well as recent increased coverage in our dataset via inclusion of Pfam domains. We also describe navigation of the website and its features. The current version (1.3) of PROCOGNATE covers 4123, 4536, 5876 structures and 377, 326, 695 superfamilies/families in CATH, SCOP and Pfam, respectively. PROCOGNATE can be accessed at: http://www.ebi.ac.uk/thornton-srv/databases/procognate/.

引用

页码：D618 / D622

页数：5

共 17 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] The ENZYME database in 2000 [J].

Bairoch, A .

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

[3] 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

[4] Cognate ligand domain mapping for enzymes [J].

Bashton, Matthew ;

Nobeli, Irene ;

Thornton, Janet M. .

JOURNAL OF MOLECULAR BIOLOGY, 2006, 364 (04) :836-852

[5] Announcing the worldwide Protein Data Bank [J].

Berman, H ;

Henrick, K ;

Nakamura, H .

NATURE STRUCTURAL BIOLOGY, 2003, 10 (12) :980-980

[6] PDBLIG: Classification of small molecular protein binding in the protein data bank [J].

Chalk, AJ ;

Worth, CL ;

Overington, JP ;

Chan, AWE .

JOURNAL OF MEDICINAL CHEMISTRY, 2004, 47 (15) :3807-3816

[7] Ligand Depot: a data warehouse for ligands bound to macromolecules [J].

Feng, ZK ;

Chen, L ;

Maddula, H ;

Akcan, O ;

Oughtred, R ;

Berman, HM ;

Westbrook, J .

BIOINFORMATICS, 2004, 20 (13) :2153-2155

[8] 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

[9] MSDsite: A database search and retrieval system for the analysis and viewing of bound ligands and active sites [J].

Golovin, A ;

Dimitropoulos, D ;

Oldfield, T ;

Rachedi, A ;

Henrick, K .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 58 (01) :190-199

[10] Databases for protein-ligand complexes [J].

Hendlich, M .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 1998, 54 :1178-1182

← 1 2 →