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Brenda

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Title: Brenda  
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Brenda

BRENDA
Content
Description molecular and biochemical information on enzymes that have been classified by the IUBMB
Contact
Research center Technische Universität Braunschweig, Department of Biochemistry and Bioinformatics
Primary citation PMID 21062828
Release date 1987
Access
Website http://www.brenda-enzymes.org
Download URL form
Web service URL soap
Tools
Miscellaneous
BRENDA

(BRaunschweig ENzyme DAtabase) is an enzyme information system representing one of the most comprehensive enzyme repositories.

Contents

  • Introduction 1
  • Content and Features 2
  • Availability 3
  • Other databases 4
  • References 5
    • Further reading 5.1
  • External links 6

Introduction

BRENDA is an electronic information resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction. Kinetic properties of the corresponding reactants; i.e., substrates and products are described in detail. BRENDA provides a web-based user interface that allows a convenient and sophisticated access to the data. BRENDA was founded in 1987 at the former German National Research Centre for Biotechnology (now: Helmholtz Centre for Infection Research) in Braunschweig and was originally published as a series of books. From 1996 to 2007, BRENDA was located at the University of Cologne. There, BRENDA developed into a publicly accessible enzyme information system.[1] In 2007, BRENDA returned to Braunschweig. Currently, BRENDA is maintained and further developed at the Department of Bioinformatics and Biochemistry at the TU Braunschweig.

BRENDA contains enzyme-specific data manually extracted from primary scientific literature and additional data derived from automatic information retrieval methods such as text mining.

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.

The latest update was performed in January 2015.

Content and Features

Database:

The database contains more than 40 data fields with enzyme-specific information on more than 4800

  • Official BRENDA website
  • Enzyme Nomenclature
  • Biobase BRENDA - The Enzyme Database

External links

  • Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D (2011). "BRENDA, the enzyme information system in 2011". Nucleic Acids Res 39 (Database issue): D670–76.  
  • 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.  
  • Schomburg D, Schomburg I, Chang A (2006). Springer Handbook of Enzymes (2nd ed.). Heidelberg: Springer. 
  • Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D (2004). "BRENDA, the enzyme database: updates and major new developments". Nucleic Acids Res 32 (Database issue): D431–433.  
  • Pharkya P, Nikolaev EV, Maranas CD (2003). "Review of the BRENDA Database". Metab Eng 5 (2): 71–73.  
  • Schomburg I, Chang A, Hofmann O, Ebeling C, Ehrentreich F, Schomburg D (2002). "BRENDA: a resource for enzyme data and metabolic information]". Trends Biochem Sci 27 (1): 54–56.  
  • Schomburg I, Chang A, Schomburg D (2002). "BRENDA, enzyme data and metabolic information". Nucleic Acids Res 30 (1): 47–49.  
  • 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. 

Further reading

  1. ^ a b c Chang A, Scheer M, Grote A, Schomburg I, Schomburg D (2008). "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009". Nucleic Acids Res 37 (Database issue): D588-D592.  
  2. ^ 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
  3. ^ Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D (2006). "BRENDA, AMENDA and FRENDA: the enzyme information system in 2007". Nucleic Acids Res 35 (Database issue): D511-D514.  

References

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:

Other databases

The usage of BRENDA is free of charge. In addition, FRENDA and AMENDA are free for non-profit users. Commercial users are in need of a license for these databases through BIOBASE.

Availability

There are several tools to obtain access to the data in BRENDA. Some of them are listed here.

Data access:

Since 2006, the data in BRENDA is supplemented with information extracted from the scientific literature by a co-occurrence based text mining approach. For this purpose, four text-mining repositories FRENDA (Full Reference ENzyme DAta), AMENDA (Automatic Mining of ENzyme DAta), DRENDA (Disease-Related ENzyme information DAtabase) and KENDA (Kinetic ENzyme DAta) were introduced. These text-mining results were derived from the titles and abstracts of all articles in the literature database PubMed.[2] [1][3]

Extensions:

, are provided. biomedical ontologies databases, as well as 3D-structure and sequence An important part of BRENDA represent the more than 107,000 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 [1]

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