BRENDA
BRENDA provides curated and mined biochemical, kinetic, structural, ligand, pathway, tissue-ontology, and disease-related information for enzymes to support functional, metabolic, and biomedical research.
Key Features:
- Data compilation and scope: Contains over 5 million manually annotated entries from more than 157,000 primary literature references covering approximately 90,000 enzymes from around 13,000 organisms.
- Data integration: Combines manual annotation with text and data mining and algorithmic predictions to assemble comprehensive enzyme functional, structural, and property data.
- Enzyme information: Records enzyme occurrence, function, kinetics, molecular properties, ligand interactions, disease associations, mutants and engineered variants, and applications in biotechnology and pharmacology.
- Disease-related data (DRENDA): Uses automatic search, text mining, and machine learning to extract and categorize enzyme–disease relationships, reporting over 910,000 EC number–disease relations.
- Pathway and structural data: Provides BRENDA Pathway Maps and three-dimensional enzyme structures with an integrated protein structure viewer.
- Associated resources: Includes FRENDA and AMENDA (PubMed abstract mining), KENDA (extraction of kinetic values), and EnzymeDetector for automatic evaluation and prediction of enzyme functions in genomes.
- BRENDA Tissue Ontology (BTO): Supplies a directed acyclic graph of over 4,600 anatomical structures linking enzymes to tissues and cell types to support text-mining.
Scientific Applications:
- Mechanistic and kinetic studies: Enables analysis of enzyme mechanisms and kinetic parameters.
- Metabolic pathway analysis and reconstruction: Supports mapping enzymes to pathway maps and pathway-level investigations.
- Disease association and therapeutics: Facilitates identification of enzyme–disease relationships and potential therapeutic or diagnostic targets using DRENDA data.
- Drug discovery and pharmacology: Provides enzyme–ligand and kinetic information relevant to inhibitor design and pharmacological research.
- Biotechnology and enzyme engineering: Informs design and evaluation of mutants and engineered enzyme variants for biotechnological applications.
- Comparative genomics and evolutionary biology: Supports functional prediction and evolutionary analyses via EnzymeDetector and curated enzyme occurrence data.
Methodology:
Data assembly uses text and data mining, machine learning–based categorization, and algorithmic predictions; automatic extraction of EC number–disease relations and kinetic values is performed via DRENDA, FRENDA, AMENDA, and KENDA; EnzymeDetector performs automatic evaluation and prediction of enzyme functions in genomes; the BRENDA Tissue Ontology is represented as a directed acyclic graph used to support text-mining.
Topics
Collections
Details
- License:
- CC-BY-4.0
- Maturity:
- Mature
- Cost:
- Free of charge (with restrictions)
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 2/3/2016
- Last Updated:
- 1/27/2025
Operations
- Database search
- Genome feature comparison
- Genome visualisation
- Literature search
- Pathway or network visualisation
- Sequence database search
- Sequence similarity search
- Structural similarity search
- Structure visualisation
- Text mining
- Transmembrane protein prediction
- Transmembrane protein visualisation
- Visualisation
Data Inputs & Outputs
Publications
Jeske L, Placzek S, Schomburg I, Chang A, Schomburg D. BRENDA in 2019: a European ELIXIR core data resource. Nucleic Acids Research. 2018;47(D1):D542-D549. doi:10.1093/nar/gky1048. PMID:30395242. PMCID:PMC6323942.
Schomburg I. BRENDA, enzyme data and metabolic information. Nucleic Acids Research. 2002;30(1):47-49. doi:10.1093/nar/30.1.47. PMID:11752250. PMCID:PMC99121.
Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, Schomburg D. The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Research. 2010;39(Database):D507-D513. doi:10.1093/nar/gkq968. PMID:21030441. PMCID:PMC3013802.
Chang A, Jeske L, Ulbrich S, Hofmann J, Koblitz J, Schomburg I, Neumann-Schaal M, Jahn D, Schomburg D. BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Research. 2020;49(D1):D498-D508. doi:10.1093/nar/gkaa1025. PMID:33211880. PMCID:PMC7779020.
Schomburg I, Jeske L, Ulbrich M, Placzek S, Chang A, Schomburg D. The BRENDA enzyme information system–From a database to an expert system. Journal of Biotechnology. 2017;261:194-206. doi:10.1016/j.jbiotec.2017.04.020. PMID:28438579.
Chang A, Schomburg I, Placzek S, Jeske L, Ulbrich M, Xiao M, Sensen CW, Schomburg D. BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Research. 2014;43(D1):D439-D446. doi:10.1093/nar/gku1068. PMID:25378310. PMCID:PMC4383907.
Chang A, Scheer M, Grote A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Research. 2009;37(Database):D588-D592. doi:10.1093/nar/gkn820. PMID:18984617. PMCID:PMC2686525.
Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Sohngen C, Stelzer M, Thiele J, Schomburg D. BRENDA, the enzyme information system in 2011. Nucleic Acids Research. 2010;39(Database):D670-D676. doi:10.1093/nar/gkq1089. PMID:21062828. PMCID:PMC3013686.
Söhngen C, Chang A, Schomburg D. Development of a classification scheme for disease-related enzyme information. BMC Bioinformatics. 2011;12(1). doi:10.1186/1471-2105-12-329. PMID:21827651. PMCID:PMC3166944.
Schomburg I. BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Research. 2004;32(90001):431D-433. doi:10.1093/nar/gkh081. PMID:14681450. PMCID:PMC308815.
Schomburg I, Chang A, Placzek S, Söhngen C, Rother M, Lang M, Munaretto C, Ulas S, Stelzer M, Grote A, Scheer M, Schomburg D. BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Research. 2012;41(D1):D764-D772. doi:10.1093/nar/gks1049. PMID:23203881. PMCID:PMC3531171.
Schomburg I, Chang A, Hofmann O, Ebeling C, Ehrentreich F, Schomburg D. BRENDA: a resource for enzyme data and metabolic information. Trends in Biochemical Sciences. 2002;27(1):54-56. doi:10.1016/s0968-0004(01)02027-8. PMID:11796225.
Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Research. 2007;35(Database):D511-D514. doi:10.1093/nar/gkl972. PMID:17202167. PMCID:PMC1899097.