BRENDA
PMID 33211880 | |
Release date | 2021 |
---|---|
Access | |
Website | http://www.brenda-enzymes.org |
Download URL | form |
Web service URL | soap |
BRENDA (The Comprehensive Enzyme Information System) is an
History
BRENDA was founded in 1987 at the former German Research Centre for Biotechnology (now the
In 2018 BRENDA was appointed to ELIXIR Core Data Resource with fundamental importance to biological and biomedical research and long-term preservation of biological data.
Updates
A major update of the data in BRENDA is performed twice a year. Besides the upgrade of its content, improvements of the user interface are also incorporated into the BRENDA database.
Content and features
Database:
The database contains more than 40 data fields with enzyme-specific information on more than 8300 EC numbers that are classified according to the IUBMB. The different data fields cover information on the enzyme's nomenclature, reaction and specificity,
An in-house development of the BRENDA team is the BRENDA tissue ontology (BTO),[4] a comprehensive, structured encyclopedia with controlled vocabulary for terms and names for tissues, organs, anatomical structures, plant parts, cell cultures, cell types, and cell lines in organisms from all taxonomic groups.
An important part of BRENDA represent the almost 260,000 enzyme ligands, which are available on their names, synonyms or via the chemical structure. The term "ligand" is used in this context to all low molecular weight compounds which interact with enzymes. These include not only metabolites of primary metabolism, co-substrates or cofactors but also enzyme inhibitors or metal ions. The origin of these molecules ranges from naturally occurring antibiotics to synthetic compounds that have been synthesized for the development of drugs or pesticides. Furthermore, cross-references to external information resources such as
Extensions:
Since 2006, the data in BRENDA is supplemented with information extracted from the
Data access:
There are several tools to obtain access to the data in BRENDA. Some of them are listed here.
- Several different query forms (e.g., quick and advanced search)
- EC tree browser
- Taxonomytree browser
- Ontologies for different biological domains (e.g., BRENDA tissue ontology, Gene Ontology)
- Thesaurus for ligand names
- Chemical substructure search engine for ligand structures
- BRENDA Pathway Maps
Download options:
Availability
The use of BRENDA is free of charge. BRENDA is subject to the terms of the Creative Commons license (CC BY 4.0).
Other databases
BRENDA provides links to several other databases with a different focus on the enzyme, e.g., metabolic function or enzyme structure. Other links lead to ontological information on the corresponding gene of the enzyme in question. Links to the literature are established with PubMed. BRENDA links to some further databases and repositories such as:
- BRENDA tissue ontology
- ExPASy
- OMIM, Domains
- IUBMBenzyme nomenclature
- KEGG
- PDB database (3D information)
- PROSITE
- SCOP
- CATH
- InterPro
- ChEBI
- Uniprot
References
- PMID 33211880.
- PMID 28438579.
- ^ PMID 18984617.
- ^ M. Gremse, A. Chang, I. Schomburg, A. Grote, M. Scheer, C. Ebeling, D. Schomburg: The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. In: Nucleic Acids Res. 39 (Database issue), 2011, S. D507–D513
- ^ 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 Res., 41 (Database issue): D764-D772
- PMID 17202167.
Further reading
- Chang A, Schomburg I, Placzek S, Jeske L, Ulbrich M, Xiao M, Sensen CW, Schomburg D (2015). "BRENDA in 2015: exciting developments in its 25th year of existence". Nucleic Acids Res. 43 (Database issue): D439–D446. PMID 25378310.
- Schomburg I, Schomburg D (2016). "BRENDA: From a database to a centre of excellence". Systembiologie.de. 10: 18–21.
- Chang A, Scheer M, Grote A, Schomburg I, Schomburg D (2009). "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009". Nucleic Acids Res. 37 (Database issue): D588–92. PMID 18984617.
- Schomburg D, Schomburg I, Chang A (2006). Springer Handbook of Enzymes (2nd ed.). Heidelberg: Springer.
- Pharkya P, Nikolaev EV, Maranas CD (2003). "Review of the BRENDA Database". Metab Eng. 5 (2): 71–73. PMID 12850129.
- Schomburg I, Chang A, Schomburg D (2002). "BRENDA, enzyme data and metabolic information". Nucleic Acids Res. 30 (1): 47–49. PMID 11752250.
- Schomburg I, Hofmann O, Bänsch C, Chang A, Schomburg D (2000). "Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine". Gene Funct Dis. 3 (4): 109–118. .