BRENDA in 2019: a European ELIXIR core data resource
Top Cited Papers
Open Access
- 5 November 2018
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 47 (D1), D542-D549
- https://doi.org/10.1093/nar/gky1048
Abstract
The BRENDA enzyme database (www.brenda-enzymes.org), recently appointed ELIXIR Core Data Resource, is the main enzyme and enzyme-ligand information system. The core database provides a comprehensive overview on enzymes. A collection of 4.3 million data for ∼84 000 enzymes manually evaluated and extracted from ∼140 000 primary literature references is combined with information obtained by text and data mining, data integration and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, predicted enzyme locations and genome annotations. Major developments are a revised ligand summary page and the structure search now including a similarity and isomer search. BKMS-react, an integrated database containing known enzyme-catalyzed reactions, is supplemented with further reactions and improved access to pathway connections. In addition to existing enzyme word maps with graphical information of enzyme specific terms, plant word maps have been developed. They show a graphical overview of terms, e.g. enzyme or plant pathogen information, connected to specific plants. An organism summary page showing all relevant information, e.g. taxonomy and synonyms linked to enzyme data, was implemented. Based on a decision by the IUBMB enzyme task force the enzyme class EC 7 has been established for ‘translocases’, enzymes that catalyze a transport of ions or metabolites across cellular membranes.Keywords
Funding Information
- German Federal Ministry of Education and Research (031A539D, 0316188B, 0316188F, 031L0078E, 031L0078G)
This publication has 37 references indexed in Scilit:
- BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDANucleic Acids Research, 2012
- DNA damage-induced cytotoxicity is mediated by the cooperative interaction of phospho-NF-κB p50 and a single nucleotide in the κB-siteNucleic Acids Research, 2012
- The NCBI Taxonomy databaseNucleic Acids Research, 2011
- SABIO-RK--database for biochemical reaction kineticsNucleic Acids Research, 2011
- Development of a classification scheme for disease-related enzyme informationBMC Bioinformatics, 2011
- BRENDA, the enzyme information system in 2011Nucleic Acids Research, 2010
- The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sourcesNucleic Acids Research, 2010
- Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificityNucleic Acids Research, 2010
- BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009Nucleic Acids Research, 2009
- UniProt: the Universal Protein knowledgebaseNucleic Acids Research, 2004