The CoFactor database: organic cofactors in enzyme catalysis

被引:54
作者
Fischer, Julia D. [1 ]
Holliday, Gemma L. [1 ]
Thornton, Janet M. [1 ]
机构
[1] EMBL EBI, Cambridge CB10 1SD, England
关键词
CLASSIFICATION; MACIE;
D O I
10.1093/bioinformatics/btq442
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database. Results: CoFactor provides a web interface to access hand-curated data extracted from the literature on organic enzyme cofactors in biocatalysis, as well as automatically collected information. CoFactor includes information on the conformational and solvent accessibility variation of the enzyme-bound cofactors, as well as mechanistic and structural information about the hosting enzymes.
引用
收藏
页码:2496 / 2497
页数:2
相关论文
共 11 条
[1]   Metal-MACiE: a database of metals involved in biological catalysis [J].
Andreini, Claudia ;
Bertini, Ivano ;
Cavallaro, Gabriele ;
Holliday, Gemma L. ;
Thornton, Janet M. .
BIOINFORMATICS, 2009, 25 (16) :2088-2089
[2]  
[Anonymous], 1993, NACCESS
[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 ;
Saux, Virginie Bulliard-Le ;
decastro, Edouard ;
Ciampina, Luciane ;
Coral, Danielle ;
Coudert, Elisabeth ;
Cusin, Isabelle ;
David, Fabrice ;
Delbard, Gwennaelle ;
Dornevil, Dolnide ;
Duek-Roggli, Paula ;
Duvaud, Severine ;
Estreicher, Anne ;
Famiglietti, Livia ;
Farriol-Mathis, Nathalie ;
Ferro, Serenella ;
Feuermann, Marc ;
Gasteiger, Elisabeth ;
Gateau, Alain ;
Gehant, Sebastian ;
Gerritsen, Vivienne ;
Gos, Arnaud ;
Gruaz-Gumowski, Nadine ;
Hinz, Ursula ;
Hulo, Chantal ;
Hulo, Nicolas ;
Innocenti, Alessandro ;
James, Janet ;
Jain, Eric ;
Jimenez, Silvia ;
Jungo, Florence ;
Junker, Vivien ;
Keller, Guillaume ;
Lachaize, Corinne ;
Lane-Guermonprez, Lydie ;
Langendijk-Genevaux, Petra .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D190-D195
[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]   E-MSD: the European Bioinformatics Institute Macromolecular Structure Database [J].
Boutselakis, H ;
Dimitropoulos, D ;
Fillon, J ;
Golovin, A ;
Henrick, K ;
Hussain, A ;
Ionides, J ;
John, M ;
Keller, PA ;
Krissinel, E ;
McNeil, P ;
Naim, A ;
Newman, R ;
Oldfield, T ;
Pineda, J ;
Rachedi, A ;
Copeland, J ;
Sitnov, A ;
Sobhany, S ;
Suarez-Uruena, A ;
Swaminathan, J ;
Tagari, M ;
Tate, J ;
Tromm, S ;
Velankar, S ;
Vranken, W .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :458-462
[6]   ChEBI:: a database and ontology for chemical entities of biological interest [J].
Degtyarenko, Kirill ;
de Matos, Paula ;
Ennis, Marcus ;
Hastings, Janna ;
Zbinden, Martin ;
McNaught, Alan ;
Alcantara, Rafael ;
Darsow, Michael ;
Guedj, Mickael ;
Ashburner, Michael .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D344-D350
[7]   MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms [J].
Holliday, Gemma L. ;
Almonacid, Daniel E. ;
Bartlett, Gail J. ;
O'Boyle, Noel M. ;
Torrance, James W. ;
Murray-Rust, Peter ;
Mitchell, John B. O. ;
Thornton, Janet M. .
NUCLEIC ACIDS RESEARCH, 2007, 35 :D515-D520
[8]   KEGG: Kyoto Encyclopedia of Genes and Genomes [J].
Kanehisa, M ;
Goto, S .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :27-30
[9]   PDBsum new things [J].
Laskowski, Roman A. .
NUCLEIC ACIDS RESEARCH, 2009, 37 :D355-D359
[10]   CATH - a hierarchic classification of protein domain structures [J].
Orengo, CA ;
Michie, AD ;
Jones, S ;
Jones, DT ;
Swindells, MB ;
Thornton, JM .
STRUCTURE, 1997, 5 (08) :1093-1108