BRENDA, the enzyme information system in 2011

被引：314

作者：

Scheer, Maurice ^{[1
]}

Grote, Andreas ^{[1
]}

Chang, Antje ^{[1
]}

Schomburg, Ida ^{[1
]}

Munaretto, Cornelia ^{[1
]}

Rother, Michael ^{[1
]}

Soehngen, Carola ^{[1
]}

Stelzer, Michael ^{[1
]}

Thiele, Juliane ^{[1
]}

Schomburg, Dietmar ^{[1
]}

机构：

[1] Tech Univ Carolo Wilhelmina Braunschweig, Dept Bioinformat & Biochem, D-38106 Braunschweig, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

关键词：

REPRESENTATION; DATABASE;

D O I：

10.1093/nar/gkq1089

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 BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information system is the main collection of enzyme functional and property data for the scientific community. The majority of the data are manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. The number of manually annotated references increased by 30% to more than 100 000, the number of ligand structures by 45% to almost 100 000. New query, analysis and data management tools were implemented to improve data processing, data presentation, data input and data access. BRENDA now provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models.

引用

页码：D670 / D676

页数：7

共 10 条

[1] The Universal Protein Resource (UniProt) in 2010 [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Antunes, Ricardo ;

Barrell, Daniel ;

Bely, Benoit ;

Bingley, Mark ;

Binns, David ;

Bower, Lawrence ;

Browne, Paul ;

Chan, Wei Mun ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Fedotov, Alexander ;

Foulger, Rebecca ;

Garavelli, John ;

Huntley, Rachael ;

Jacobsen, Julius ;

Kleen, Michael ;

Laiho, Kati ;

Leinonen, Rasko ;

Legge, Duncan ;

Lin, Quan ;

Liu, Wudong ;

Luo, Jie ;

Orchard, Sandra ;

Patient, Samuel ;

Poggioli, Diego ;

Pruess, Manuela ;

Corbett, Matt ;

di Martino, Giuseppe ;

Donnelly, Mike ;

van Rensburg, Pieter ;

Bairoch, Amos ;

Bougueleret, Lydie ;

Xenarios, Ioannis ;

Altairac, Severine ;

Auchincloss, Andrea ;

Argoud-Puy, Ghislaine ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bolleman, Jerven ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D142-D148

[2] The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases [J].

Caspi, Ron ;

Altman, Tomer ;

Dale, Joseph M. ;

Dreher, Kate ;

Fulcher, Carol A. ;

Gilham, Fred ;

Kaipa, Pallavi ;

Karthikeyan, Athikkattuvalasu S. ;

Kothari, Anamika ;

Krummenacker, Markus ;

Latendresse, Mario ;

Mueller, Lukas A. ;

Paley, Suzanne ;

Popescu, Liviu ;

Pujar, Anuradha ;

Shearer, Alexander G. ;

Zhang, Peifen ;

Karp, Peter D. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D473-D479

[3] BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 [J].

Chang, Antje ;

Scheer, Maurice ;

Grote, Andreas ;

Schomburg, Ida ;

Schomburg, Dietmar .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D588-D592

[4] The systems biology markup language (SBML):: a medium for representation and exchange of biochemical network models [J].

Hucka, M ;

Finney, A ;

Sauro, HM ;

Bolouri, H ;

Doyle, JC ;

Kitano, H ;

Arkin, AP ;

Bornstein, BJ ;

Bray, D ;

Cornish-Bowden, A ;

Cuellar, AA ;

Dronov, S ;

Gilles, ED ;

Ginkel, M ;

Gor, V ;

Goryanin, II ;

Hedley, WJ ;

Hodgman, TC ;

Hofmeyr, JH ;

Hunter, PJ ;

Juty, NS ;

Kasberger, JL ;

Kremling, A ;

Kummer, U ;

Le Novère, N ;

Loew, LM ;

Lucio, D ;

Mendes, P ;

Minch, E ;

Mjolsness, ED ;

Nakayama, Y ;

Nelson, MR ;

Nielsen, PF ;

Sakurada, T ;

Schaff, JC ;

Shapiro, BE ;

Shimizu, TS ;

Spence, HD ;

Stelling, J ;

Takahashi, K ;

Tomita, M ;

Wagner, J ;

Wang, J .

BIOINFORMATICS, 2003, 19 (04) :524-531

[5] KEGG for representation and analysis of molecular networks involving diseases and drugs [J].

Kanehisa, Minoru ;

Goto, Susumu ;

Furumichi, Miho ;

Tanabe, Mao ;

Hirakawa, Mika .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D355-D360

[6] Database resources of the National Center for Biotechnology Information [J].

Sayers, Eric W. ;

Barrett, Tanya ;

Benson, Dennis A. ;

Bolton, Evan ;

Bryant, Stephen H. ;

Canese, Kathi ;

Chetvernin, Vyacheslav ;

Church, Deanna M. ;

DiCuccio, Michael ;

Federhen, Scott ;

Feolo, Michael ;

Geer, Lewis Y. ;

Helmberg, Wolfgang ;

Kapustin, Yuri ;

Landsman, David ;

Lipman, David J. ;

Lu, Zhiyong ;

Madden, Thomas L. ;

Madej, Tom ;

Maglott, Donna R. ;

Marchler-Bauer, Aron ;

Miller, Vadim ;

Mizrachi, Ilene ;

Ostell, James ;

Panchenko, Anna ;

Pruitt, Kim D. ;

Schuler, Gregory D. ;

Sequeira, Edwin ;

Sherry, Stephen T. ;

Shumway, Martin ;

Sirotkin, Karl ;

Slotta, Douglas ;

Souvorov, Alexandre ;

Starchenko, Grigory ;

Tatusova, Tatiana A. ;

Wagner, Lukas ;

Wang, Yanli ;

Wilbur, W. John ;

Yaschenko, Eugene ;

Ye, Jian .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D5-D16

[7]

Schomburg D., 2001, SPRINGER HDB ENZYMES, V2nd

[8]

SCHOMBURG I, 2000, GENE FUNCT DIS, V3, P109

[9]

Stein SE, 2003, PROCEEDINGS OF THE 2003 INTERNATIONAL CHEMICAL INFORMATION CONFERENCE, P131

[10]

Velankar S, 2010, NUCLEIC ACIDS RES, V38, pD308, DOI [10.1093/nar/gkp916, 10.1093/nar/gkq985]

← 1 →