BRENDA, the ELIXIR core data resource in 2021: new developments and updates

被引:429
作者
Chang, Antje [1 ]
Jeske, Lisa [1 ]
Ulbrich, Sandra [1 ]
Hofmann, Julia [1 ]
Koblitz, Julia [2 ]
Schomburg, Ida [1 ]
Neumann-Schaal, Meina [2 ]
Jahn, Dieter [1 ]
Schomburg, Dietmar [1 ]
机构
[1] Tech Univ Carolo Wilhelmina Braunschweig, Braunschweig Integrated Ctr Syst Biol BRICS, Rebenring 56, D-38106 Braunschweig, Germany
[2] Leibniz Inst DSMZ German Collect Microorganisms &, Inhoffenstr 7 B, D-38124 Braunschweig, Germany
关键词
CLASSIFICATION; PERSPECTIVES; PROTEINS; TOOLS;
D O I
10.1093/nar/gkaa1025
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 enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the integration of newly discovered enzymes. The main part contains >5 million data for similar to 90 000 enzymes from similar to 13 000 organisms, manually extracted from similar to 157 000 primary literature references, combined with information of text and data mining, data integration, and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, genome annotations, ligand information, taxonomic, bibliographic, and kinetic data. BRENDA offers an easy access to enzyme information from quick to advanced searches, text- and structured-based queries for enzyme-ligand interactions, word maps, and visualization of enzyme data. The BRENDA Pathway Maps are completely revised and updated for an enhanced interactive and intuitive usability. The new design of the Enzyme Summary Page provides an improved access to each individual enzyme. A new protein structure 3D viewer was integrated. The prediction of the intracellular localization of eukaryotic enzymes has been implemented. The new EnzymeDetector combines BRENDA enzyme annotations with protein and genome databases for the detection of eukaryotic and prokaryotic enzymes.
引用
收藏
页码:D498 / D508
页数:11
相关论文
共 35 条
[1]  
Acland A, 2013, NUCLEIC ACIDS RES, V41, pD8, DOI [10.1093/nar/gks1189, 10.1093/nar/gkx1095, 10.1093/nar/gkq1172]
[2]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[3]   Untitled [J].
Bateman, Alex .
NUCLEIC ACIDS RESEARCH, 2006, 34 :D1-D1
[4]   RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy [J].
Burley, Stephen K. ;
Berman, Helen M. ;
Bhikadiya, Charmi ;
Bi, Chunxiao ;
Chen, Li ;
Di Costanzo, Luigi ;
Christie, Cole ;
Dalenberg, Ken ;
Duarte, Jose M. ;
Dutta, Shuchismita ;
Feng, Zukang ;
Ghosh, Sutapa ;
Goodsell, David S. ;
Green, Rachel K. ;
Guranovic, Vladimir ;
Guzenko, Dmytro ;
Hudson, Brian P. ;
Kalro, Tara ;
Liang, Yuhe ;
Lowe, Robert ;
Namkoong, Harry ;
Peisach, Ezra ;
Periskova, Irina ;
Prlic, Andreas ;
Randle, Chris ;
Rose, Alexander ;
Rose, Peter ;
Sala, Raul ;
Sekharan, Monica ;
Shao, Chenghua ;
Tan, Lihua ;
Tao, Yi-Ping ;
Valasatava, Yana ;
Voigt, Maria ;
Westbrook, John ;
Woo, Jesse ;
Yang, Huanwang ;
Young, Jasmine ;
Zhuravleva, Marina ;
Zardecki, Christine .
NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D464-D474
[5]   The MetaCyc database of metabolic pathways and enzymes [J].
Caspi, Ron ;
Billington, Richard ;
Fulcher, Carol A. ;
Keseler, Ingrid M. ;
Kothari, Anamika ;
Krummenacker, Markus ;
Latendresse, Mario ;
Midford, Peter E. ;
Ong, Quang ;
Ong, Wai Kit ;
Paley, Suzanne ;
Subhraveti, Pallavi ;
Karp, Peter D. .
NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) :D633-D639
[6]   SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database [J].
Chandonia, John-Marc ;
Fox, Naomi K. ;
Brenner, Steven E. .
JOURNAL OF MOLECULAR BIOLOGY, 2017, 429 (03) :348-355
[7]   BRENDA in 2015: exciting developments in its 25th year of existence [J].
Chang, Antje ;
Schomburg, Ida ;
Placzek, Sandra ;
Jeske, Lisa ;
Ulbrich, Marcus ;
Xiao, Mei ;
Sensen, Christoph W. ;
Schomburg, Dietmar .
NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D439-D446
[8]   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
[9]   The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences [J].
Drysdale, Rachel ;
Cook, Charles E. ;
Petryszak, Robert ;
Baillie-Gerritsen, Vivienne ;
Barlow, Mary ;
Gasteiger, Elisabeth ;
Gruhl, Franziska ;
Haas, Jurgen ;
Lanfear, Jerry ;
Lopez, Rodrigo ;
Redaschi, Nicole ;
Stockinger, Heinz ;
Teixeira, Daniel ;
Venkatesan, Aravind ;
Blomberg, Niklas ;
Durinx, Christine ;
McEntyre, Johanna .
BIOINFORMATICS, 2020, 36 (08) :2636-2642
[10]   BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation [J].
Dudek, Christian-Alexander ;
Dannheim, Henning ;
Schomburg, Dietmar .
PLOS ONE, 2017, 12 (07)