BRENDA

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BRENDA ( BR aunschweig EN zyme DA tabase) is one of the world's most comprehensive and important online biochemistry databases for biochemical and molecular biological data on enzymes and metabolic pathways.

BRENDA is an online enzyme information system that contains biochemical and molecular biological data and information on all enzymes classified by the enzyme commission of the International Union of Biochemistry and Molecular Biology (IUBMB). The IUBMB classifies enzymes according to their catalyzed chemical reaction and assigns them to an "Enzyme Class" number ( EC number ), the properties and functions of which are described in detail in BRENDA.

The enzyme-specific data and information in BRENDA are manually annotated from scientific literature by biochemists, biologists and chemists. In addition, computer-aided methods are used to obtain information such as B. Text mining to expand the information content in BRENDA. The BRENDA website offers users quick and easy access to this data with the help of various search masks.

BRENDA was founded in 1987 at what was then GBF - Society for Biotechnological Research - (today: Helmholtz Center for Infection Research HZI ) in Braunschweig by Dietmar Schomburg . Initially, BRENDA was published as a book series, until the data collection was further developed in his group from 1996 to 2007 at the University of Cologne into one of the world's most popular online information systems for biochemistry . BRENDA has been back in Braunschweig since 2007 and is maintained and further developed at the Technical University of Braunschweig in the Bioinformatics and Biochemistry Department.

The data in BRENDA is updated every six months. In addition to the integration of new data, extensions and corrections are made to the Internet presentation, the search masks and the programs in BRENDA.

Content and functionality

Database:

The IUBMB Enzyme Commission has currently classified more than 7000 EC numbers. For the BRENDA database, enzyme-specific information is extracted from the literature, assigned to the EC numbers and stored in more than 40 data and information fields. This information includes: a. the nomenclature of the enzymes, the catalyzed reactions and their specificity, substrates and products, inhibitors and activating substances and cofactors. In addition, information on the enzyme structure, isolation and purification, enzyme stability, kinetic parameters, such as z. B. Km values and turnover rate (" turnover number "), the occurrence and the intracellular localization, as well as mutagenesis studies are offered. BRENDA currently contains manually annotated data from over 140,000 different scientific articles. Each entry in the database is linked to at least one literature reference and the organism from which the enzyme was isolated. If the protein sequence is known and published, the data can be assigned to a sequence using the UniProt ID.

An in-house development of the BRENDA Group is the BRENDA Tissue Ontology (BTO), a comprehensive, structured encyclopedia with a controlled vocabulary for terms and designations for tissue, organs, anatomical structures, plant parts, cell cultures, cell types and cell lines in organisms from all taxonomic groups. An important part of BRENDA are the more than 110,000 enzyme ligands that are available by name, synonyms or chemical structure. The term “ligand” is used in this context for all low molecular weight compounds that interact with enzymes. These include metabolites of primary metabolism, cosubstrates or cofactors as well as enzyme inhibitors or metal ions. The origins of these molecules range from naturally occurring antibiotics to synthetic compounds synthesized for drug or pesticide development.

In addition to the manually annotated information, BRENDA offers links to external information systems and databases, such as B. Protein sequence and protein structure databases, literature databases, ontologies etc.

Extensions:

Since 2006, in addition to the manually extracted data in BRENDA, information that can be obtained using computer-aided methods has also been added. For this purpose, BRENDA has been expanded to include four new information systems: FRENDA (Full Reference ENzyme DAta), AMENDA (Automatic Mining of ENzyme DAta), DRENDA (Disease-Related ENzyme information DAtabase) and KENDA (Kinetic ENzyme DAta). The PubMed literature database serves as the basis for the text mining methods . In order to obtain the information relevant for BRENDA, all titles and short descriptions of the scientific articles are searched in PubMed for certain text modules and terms, saved and prepared for BRENDA.

Access to BRENDA:

The BRENDA database offers various options for quick and convenient access to data and information:

WEB browser based:

  • various search masks (including "Quick Search" and "Advanced Search")
  • EC-Tree Browser
  • TaxTree Browser
  • Substructure Search (search for chemical compounds that act as substrates, products, cofactors and inhibitors)
  • Name-based search for enzymes or chemical compounds that interact with enzymes - e.g. B. as substrates, cofactors or inhibitors of enzyme-catalyzed reactions

Other:

Availability

Use of the BRENDA is free of charge, but requires registration. FRENDA, AMENDA, KENDA and DRENDA are free for non-commercial users. Commercial users need to purchase a license for these databases. These are available from Biobase GmbH.

Other databases

In addition to BRENDA, there are databases that have a slightly different focus on enzymes, e.g. B. metabolic function or enzyme structure. BRENDA offers links to these databases. Some of these databases are given here:

Individual evidence

  1. a b c A. Chang, M. Scheer, A. Grote, I. Schomburg, D. Schomburg: BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. In: Nucleic Acids Res . 37 (Database issue), pp. D588-D592
  2. M. Gremse, A. Chang, I. Schomburg, A. Grote, M. Scheer, C. Ebeling, D. Schomburg: The BRENDA tissue ontology (BTO): the first all-integra ting ontology of all organisms for enzyme sources. In: Nucleic Acids Res. 39 (Database issue), 2011, pp. D507-D513
  3. ^ I. Schomburg, A. Chang, S. Placzek, C. Söhngen, M. Rother, M. Lang, C. Munaretto, S. Ulas, M. Stelzer, A. Grote, M. Scheer, D. Schomburg: BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. In: Nucleic Acids Res. 41 (Database issue), pp. D764-D772
  4. J. Barthelmes, C. Ebeling, A. Chang, I. Schomburg, D. Schomburg: BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. In: Nucleic Acids Res. 35 (Database issue), p. D511- D514
  5. M. Scheer, A. Grote, A. Chang, I. Schomburg, C. Munaretto, M. Rother, C. Söhngen, M. Stelzer, J. Thiele, D. Schomburg: BRENDA, the enzyme information system in 2011. In: Nucleic Acids Res. 39 (Database issue), pp. D670-D676

literature

  • D. Schomburg, I. Schomburg, A. Chang: Springer Handbook of Enzymes . 2nd Edition. Springer, Heidelberg 2006.
  • I. Schomburg, A. Chang, C. Ebeling, M. Gremse, C. Heldt, G. Huhn, D. Schomburg: BRENDA, the enzyme database: updates and major new developments . In: Nucleic Acids Res . tape 32 , Database issue, 2004, p. D431-3 .
  • P. Pharkya, EV Nikolaev, CD Maranas: Review of the BRENDA Database . In: Metab Eng . tape 5 , no. 2 , 2003, p. 71-73 , doi : 10.1016 / S1096-7176 (03) 00008-9 .
  • I. Schomburg, A. Chang, O. Hofmann, C. Ebeling, F. Ehrentreich, D. Schomburg: BRENDA: a resource for enzyme data and metabolic information . In: Trends Biochem Sci . tape 27 , no. 1 , 2002, p. 54-56 , doi : 10.1016 / S0968-0004 (01) 02027-8 .
  • I. Schomburg, A. Chang, D. Schomburg: BRENDA, enzyme data and metabolic information . In: Nucleic Acids Res . tape 30 , 2002, pp. 47-49 .
  • I. Schomburg, O. Hofmann, C. Bänsch, A. Chang, D. Schomburg: Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine . In: Gene Funct Dis . tape 3 , no. 4 , 2000, pp. 109-118 .

Web links