Frequently Asked Questions
- When are new data and information in BRENDA released?
- How does the BRENDA team collect the data and information for the database?
- Does BRENDA contain all kind of enzymes?
- Does BRENDA include information on mutated enzymes?
- How to access the data and information in BRENDA?
- How to download search results?
- How to download BRENDA?
- What is BRENDA?
- What means BRENDA Input?
- What are Ligands in BRENDA?
- What happens to not (yet) classified enzymes?
- What are the Recommendations of the IUBMB for enzymes?
- What are commentary fields?
- What is KENDA?
- What is DRENDA?
- What is FRENDA?
- What is AMENDA?
- What are EC Numbers, which contain a "B" in the digits (i.e. EC 1.1.4.B1)
When are new data and information in BRENDA released?
BRENDA is updated twice a year. The new release is avalailable in July and January.
How does the BRENDA team collect the data and information for the database?
The main part of BRENDA are manually annoted data and information from literature references. Additionally text-mining tools (AMENDA; FRENDA; DRENDA; KENDA) are implemented to complete the database. Further information are direct links to other datebases, such as UniProt, PDB or PubMed.
Does BRENDA contain all kind of enzymes?
No, the content is based on the enzyme classification system of the IUBMB (International Union of Biochemistry and Molecular Biology). All enzymes according to the scheme of the Enzyme Nomenclature Committee are integrated in BRENDA.
Does BRENDA include information on mutated enzymes?
Yes, information on mutated enzymes can be found in the information field "ENGINEERING" which comprises results of site-directed mutagenesis experiments, deletion, knock-out mutants, amino acid exchanges etc.
How to access the data and information in BRENDA?
The user can either use
- Quick Search on the main page
- Advanced Search for combined searches
- Fulltext search, including comments
- TaxTree Explorer
- EC Explorer
- Ontology Explorer
- Genome Explorer
- Substructure Search
- Sequence Search
How to download search results?
The results of a "Quick Search" are downloadable as tab stop separated values in a cvs-format.
How to download BRENDA?
All manually annotated BRENDA data can be downloaded as a single text file. See section 'Download'.
What is BRENDA?
BRENDA is one of the most comprehensive enzyme information sources in life science, with convenient and easy searchable data extracted from the primary literature:
- classification and nomenclature
- reaction and specificity
- functional and kinetic parameters
- organism-related information
- enzyme structure and stability
- supplemented with text-mining tools for
- Source/Tissues and Localization
- Disease-related enzyme information
- Kinetic values and expressions
What means BRENDA Input?
If an information is not avalailable in BRENDA or a reference is missing the user has the opportunity to fill out a form and afterwards send it to the BRENDA team to include it into the database.
What are Ligands in BRENDA?
The term „Ligands“ in BRENDA refer to all compounds which interact with enzymes. They can be substrates and products, cofactors, inhibitors, metal ions or activating compounds. These are small molecules or macromolecules such as proteins, DNA or RNA. The ligands and their roles are presented in the "Ligand Summary Page" and can also be found via "Quick Search" or the "Substructure Search" tool.
What happens to not (yet) classified enzymes?
Enzymes, which are not classified according to the IUBMB enzyme classification system are not assigned to EC numbers. If an enzyme is sufficiently biochemically characterized the BRENDA team prepares a proposal to submit it the IUBMB. It takes about 2 months, passing through several review and approval steps until the enzyme finally gets its EC Number. In the meantime BRENDA includes the enzyme as "preliminary BRENDA-supplied EC number".
What are the Recommendations of the IUBMB for enzymes?
The Recommended or Common Name of enzymes is given by the IUBMB as well as the "Systematic Name" and the "Catalysed Reaction", on which the enzyme classification is based.
What are commentary fields?
Most of the information fields in BRENDA contain commentary fields in which the main entry is explained in more detail or supplemental information to the method supplied or the reaction conditions are included
What is KENDA?
KENDA is the result of a text-mining approach to include addtional functional enzyme data by extracting kinetic values and kinetic expressions from more than 2.2 million PubMed abstracts.
What is DRENDA?
DRENDA provides disease-related enzyme information analysing PubMed abstracts by a text-mining approach using MeSH terms. The results are classified into 4 categories causal interaction, therapeutic application, diagnostic usage, and ongoing research.
What is FRENDA?
FRENDA provides all references found in PubMed containing combinations of enzyme names and organisms.
What is AMENDA?
AMENDA is a subset of FRENDA, additionally providing organism-specific information on the enzyme sources and the subcelluar localization.
What are EC Numbers, which contain a "B" in the digits (i.e. EC 1.1.4.B1)?
Enzymes, which are not classified according to the IUBMB enzyme classification system are not (yet) assigned to EC numbers. If an enzyme is sufficiently biochemically characterized the BRENDA team prepares a data set and includes the enzyme as "preliminary BRENDA-supplied EC number". For classification purposes a proposal is prepared to submit it the IUBMB. It takes about 2 months, passing through several review and approval steps until the enzyme finally gets its EC Number.