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'''BRENDA''' ('''BRaunschweig ENzyme DAtabase''') is an enzyme information system comprising one of the largest and most comprehensive [[enzyme]] databases.
'''BRENDA''' ('''BRaunschweig ENzyme DAtabase''') is an enzyme information system representing one of the most comprehensive [[enzyme]] repositories.




== Introduction ==
== Introduction ==
BRENDA is an electronic information ressource with a large [[Database_system|database system]] that comprises [[Biomolecule|molecular]] and [[Biochemistry|biochemical]] information on enzymes which have been classified by the [[IUBMB]]. Every [[List_of_enzymes|classified]] [[enzyme]] is characterized with respect to the [[Catalysis|catalyzed]] [[Biochemistry|biochemical]] [[Chemical_reaction|reactions]]. The kinetic properties of the corresponding [[reactants]] the [[Substrate (biochemistry) |substrates]] and [[Product (chemistry)|products]] are described in detail.
BRENDA is an electronic information ressource that comprises [[Biomolecule|molecular]] and [[Biochemistry|biochemical]] information on enzymes which have been classified by the [[IUBMB]]. Every [[List_of_enzymes|classified]] [[enzyme]] is characterized with respect to its [[Catalysis|catalyzed]] [[Biochemistry|biochemical]] [[Chemical_reaction|reaction]]. Kinetic properties of the corresponding [[reactants]] i.e. [[Substrate (biochemistry) |substrates]] and [[Product (chemistry)|products]] are described in detail.
In addition, BRENDA provides a [[World_Wide_Web|web]]-based [[User_interface|user interface]] which serves as a query system for the underlying [[Database|database]].
BRENDA provides a web-based [[User_interface|user interface]] that allows a convenient and sophisticated [http://www.brenda-enzymes.org access] to the data.
The BRENDA database itself was founded in 1987 at the former German National Research Centre for Biotechnology (now: [[Helmholtz Centre for Infection Research]]) in [[Braunschweig]]. It was originally published as a series of books and was continuously improved at the [[University of Cologne]] from 1996 to 2007 where it was developed into a publicly accessible [[Relational_database|relational database]] <ref name="Chang2009">Chang A, Scheer M, Grote A, Schomburg I, Schomburg D: "[http://nar.oxfordjournals.org/cgi/content/full/gkn820v1 BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009]", ''Nucleic Acids Res.'', 37 (Database issue): D588-D592</ref>. Since 2007, BRENDA is back in [[Braunschweig]]: it is maintained and developed at the Department of Bioinformatics and Biochemistry at the [[TU Braunschweig|TU Braunschweig]] by a team of [[Biochemist|biochemists]], [[Biologist|biologists]] and [[Bioinformatician|bioinformaticians]].
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]]. Here, BRENDA developed into a publicly accessible enzyme information system<ref name="Chang2009">Chang A, Scheer M, Grote A, Schomburg I, Schomburg D: "[http://nar.oxfordjournals.org/cgi/content/full/gkn820v1 BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009]", ''Nucleic Acids Res.'', 37 (Database issue): D588-D592</ref>. In 2007, BRENDA returned to [[Braunschweig]]. Currently, BRENDA is maintained and further developed at the Department of Bioinformatics and Biochemistry at the [[TU Braunschweig|TU Braunschweig]].


BRENDA covers both, [[Enzyme|enzyme]]-specific data manually extracted from the [[Scientific_literature|primary scientific literature]] and data obtained from automatic [[Information_retrieval|information retrieval]] methods such as [[Text_mining|text mining]]. Formal and consistency checks are done by computer programs and each data set is checked manually.
BRENDA contains enzyme-specific data manually extracted from [[Scientific_literature|primary scientific literature]] and additional data derived from automatic [[Information_retrieval|information retrieval]] methods such as [[Text_mining|text mining]].


A major update of the data in BRENDA is performed twice a year. Besides the upgrade of its content also improvements of the user interface are incorporated into the BRENDA database.
Twice a year BRENDA undergoes a major update resulting in a significant upgrade of its [[database]] content and in an improvement of its [[Information_technology|information technology]] part which includes the [[World_Wide_Web|web]]-based [[User_interface|user interface]] and the automatic [[information retrieval]] from other [[database|databases]] or the [[Scientific_literature|scientific literature]] .


The latest update was performed in January 2009.
The latest update was performed in January 2009.


==Database Content and Features==
== Content and Features ==


Database:
'''Database:'''


The database covers more than 40 data fields with enzyme-specific information on more than 4800 [[EC_number|EC numbers] that have been classified according to the [[International_Union_of_Biochemistry_and_Molecular_Biology|IUBMB]] scheme. The different data fields cover the enzyme nomenclature, reaction and specificity, enzyme structure, [[isolation]]/preparation, enzyme [[stability]], kinetic parameters such as pH optimum and turnover number, occurrence/localization, mutants and engineered enzyme, the application of enzymes, and ligand-related data. These [[data]] were all manually curated from almost 85,000 different [[Scientific_literature|primary literature]] references. Each [[enzyme]] entry is clearly linked to at least one literature reference, its source [[organism]] and, where available, to the protein sequence of the [[enzyme]]<ref name="Chang2009">Chang A, Scheer M, Grote A, Schomburg I, Schomburg D: "[http://nar.oxfordjournals.org/cgi/content/full/gkn820v1 BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009]", ''Nucleic Acids Res.'', 37 (Database issue): D588-D592</ref>. In addition, cross-references to external information resources such as sequence and 3D-structure [[database|databases]] as well as biomedical [[ontology|ontologies]] are provided.
The database contains more than 40 data fields with enzyme-specific information on more than 4800 [[EC_number|EC numbers]] that are classified according to the [[International_Union_of_Biochemistry_and_Molecular_Biology|IUBMB]].
The different data fields cover information on the enzyme´s nomenclature, reaction and specificity, enzyme structure, isolation and preparation, enzyme stability, kinetic parameters such as Km value and turnover number, occurrence and localization, mutants and engineered enzymes, application of enzymes and ligand-related data. The data originates from almost 85,000 different [[Scientific_literature|scientific articles]]. Each enzyme entry is clearly linked to at least one literature reference, its source [[organism]] and, where available, to the protein sequence of the enzyme<ref name="Chang2009">Chang A, Scheer M, Grote A, Schomburg I, Schomburg D: "[http://nar.oxfordjournals.org/cgi/content/full/gkn820v1 BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009]", ''Nucleic Acids Res.'', 37 (Database issue): D588-D592</ref>. Furthermore, cross-references to external information resources such as sequence and 3D-structure databases as well as biomedical [[ontology|ontologies]] are provided.


'''Extensions:'''
Database extensions:


As of autumn 2006, in addition to the manually curated data, BRENDA is supplemented with information extracted from the scientific literature by a co-occurence based [[Biomedical_text_mining|text mining]] approach. For this purpose two textmining repositories FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) were introduced that represent a complete survey on enzyme data derived from the titles and abstracts of all articles from the literature database PubMed <ref name="Chang2009">Chang A, Scheer M, Grote A, Schomburg I, Schomburg D: "[http://nar.oxfordjournals.org/cgi/content/full/gkn820v1 BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009]", ''Nucleic Acids Res.'', 37 (Database issue): D588-D592</ref> <ref name="Barthelmes2007">Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D: "[http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D511 BRENDA, AMENDA and FRENDA: the enzyme information system in 2007]", ''Nucleic Acids Res.'', 35 (Database issue): D511-D514</ref>.
Since 2006 the data in BRENDA is supplemented with information extracted from the scientific literature by a co-occurence based [[Biomedical_text_mining|text mining]] approach. For this purpose two textmining repositories FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) were introduced. These textmining results were derived from titles and abstracts of all articles in the literature database [[PubMed]] <ref name="Chang2009">Chang A, Scheer M, Grote A, Schomburg I, Schomburg D: "[http://nar.oxfordjournals.org/cgi/content/full/gkn820v1 BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009]", ''Nucleic Acids Res.'', 37 (Database issue): D588-D592</ref> <ref name="Barthelmes2007">Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D: "[http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D511 BRENDA, AMENDA and FRENDA: the enzyme information system in 2007]", ''Nucleic Acids Res.'', 35 (Database issue): D511-D514</ref>.


'''Data access:'''


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


* Several different query forms (e.g. quick and advanced search)
Features of the web interface of BRENDA:
* [[SOAP]| SOAP-Interface]

* EC-tree browser
* EC-tree browser
* Taxonomy-tree browser
* Taxonomy-tree browser
* Chemical substructure search engine for ligand structures
* Chemical substructure search engine for ligand structures
* Ontologies for different data fields
* Development of controlled vocabulary
* Ontology for some information fields
* Thesaurus for ligand names
* Thesaurus for ligand names


==Usage==
== Availability ==
The database covers 40 data fields with information about nomenclature, reaction and specificity, enzyme structure, [[isolation]]/preparation, [[stability]], literature references and cross references to sequence and 3D-structure data banks.


The BRENDA resource is available free of charge. The FRENDA and AMENDA databases is availabel free of charge for non-profit users. Commercial useres require a license for thes databases. For use the latter tow require registration by email. The database can be searched by EC number, enzyme name, organism, or an advanced search combining these terms.
The usage of BRENDA is free of charge. FRENDA and AMENDA are only free of charge for non-profit users. Commercial users are in need of a license for these databases.
===Example===
As an example you can use the quick search to search for [[pyruvate dehydrogenase]]. This search gives several forms of the enzyme. If you click on pyruvate dehydrogenase (NADP+) it takes you to a page it gives you information on:
* Enzyme nomenclature
* Enzyme ligand interactions
* Functional parameters
* Organism related information
* Enzyme structure
* Molecular properties
* Bibliography/links/Disease


⚫
== Other databases ==
This page also shows all the [[organism]]s that contain this [[enzyme]]. If you wanted to determine the pyruvate dehydrogenase enzyme found in humans you can use the advance search using this query:
enzyme name = pyruvate dehydrogenase
organism = homo sapiens


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]].
This query gives the result pyruvate dehydrogenase (lipoamide).
BRENDA links to some further databases and repositories such as:


Other methods of searching include full text search, substructure search, TaxTree search (search an organism in taxonomy tree), search the [[EC number|EC tree]] and it is possible to do a sequence search.

⚫
==Other databases==
BRENDA also links to other databases. Including [[KEGG]] which provides information about the pathway that the enzyme is involved in. It also links to gene ontology information through the GO website. There is also links to the literature through PubMed. Other databases that BRENDA link to include:
* [[ExPASy]]
* [[ExPASy]]
* [[National Center for Biotechnology Information|NCBI]] databases (Protein, nucleotide, structure, genome, [[Mendelian Inheritance in Man|OMIM]], Domains
* [[National Center for Biotechnology Information|NCBI]] databases (Protein, nucleotide, structure, genome, [[Mendelian Inheritance in Man|OMIM]], Domains
* [[IUBMB]] enzyme nomenclature
* [[IUBMB]] enzyme nomenclature
⚫
* [[KEGG]]
* [[Protein Data Bank|PDB]] database (3D information)
* [[Protein Data Bank|PDB]] database (3D information)
* [[PROSITE]]
* [[PROSITE]]
⚫
* [[SYSTERS]]
* Protein mutant database
* [[Structural Classification of Proteins|SCOP]]
* [[Structural Classification of Proteins|SCOP]]
* [[CATH]]
* [[CATH]]
* [[InterPro]]
* [[InterPro]]
* [[ChEBI]]
* [[Uniprot]]


⚫
== References ==



⚫
==References==
{{reflist}}
{{reflist}}

===Further reading===
=== Further reading ===

*{{cite journal |author=Schomburg I, Hofmann O, Bänsch C, Chang A, Schomburg D |year=2000 |title=Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine |journal=Gene Funct Dis |volume=3 |issue=4 |pages=109-118}}
*{{cite journal |author=Schomburg I, Hofmann O, Bänsch C, Chang A, Schomburg D |year=2000 |title=Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine |journal=Gene Funct Dis |volume=3 |issue=4 |pages=109-118}}
*{{cite book |author=Schomburg D, Schomburg I |year=2001 |title=Springer Handbook of Enzymes |edition=2nd Ed |publisher=Springer |place=Heidelberg}}
*{{cite journal |author=Schomburg I, Chang A, Schomburg D |year=2002 |title=[http://nar.oxfordjournals.org/cgi/content/full/30/1/47 BRENDA, enzyme data and metabolic information] |journal=Nucleic Acids Res |volume=30 |pages=47-49}}
*{{cite journal |author=Schomburg I, Chang A, Schomburg D |year=2002 |title=BRENDA, enzyme data and metabolic information |journal=Nucleic Acids Res |volume=30 |pages=47-49}}
*{{cite journal |author=Schomburg I, Chang A, Hofmann O, Ebeling C, Ehrentreich F, Schomburg D |year=2002 |title=[http://dx.doi.org/10.1016/S0968-0004(01)02027-8 BRENDA: a resource for enzyme data and metabolic information] |journal=Trends Biochem Sci |volume=27 |issue=1 |pages=54-56}}
*{{cite journal |author=Schomburg I, Chang A, Hofmann O, Ebeling C, Ehrentreich F, Schomburg D |year=2002 |title=BRENDA: a resource for enzyme data and metabolic information |journal=Trends Biochem Sci |volume=27 |issue=1 |pages=54-56}}
*{{cite journal |author=Pharkya P, Nikolaev EV, Maranas CD |year=2003 |title=[http://dx.doi.org/10.1016/S1096-7176(03)00008-9 Review of the BRENDA Database] |journal=Metab Eng |volume=5 |issue=2 |pages=71-73}}
*{{cite journal |author=Pharkya P, Nikolaev EV, Maranas CD |year=2003 |title=Review of the BRENDA Database |journal=Metab Eng |volume=5 |issue=2 |pages=71-73}}
*{{cite journal |author=Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D |year=2004 |title=[http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D431 BRENDA, the enzyme database: updates and major new developments] |journal=Nucleic Acids Res |volume=32 |issue=Database issue |pages=D431-3}}
*{{cite journal |author=Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D |year=2004 |title=BRENDA, the enzyme database: updates and major new developments |journal=Nucleic Acids Res |volume=32 |issue=Database issue |pages=D431-3}}
*{{cite book |author=Schomburg D, Schomburg I, Chang A |year=2006 |title=Springer Handbook of Enzymes |edition=2nd |publisher=Springer |place=Heidelberg}}

⚫
== External links ==


⚫
==External links==
* [http://www.brenda-enzymes.org Official BRENDA website]
* [http://www.brenda-enzymes.org Official BRENDA website]
⚫
* [http://www.chem.qmul.ac.uk/iubmb/enzyme/ Enzyme Nomenclature]
* [http://www.empproject.com/ EMP: Enzymes and Metabolic Pathways database]
* [http://www.empproject.com/ EMP: Enzymes and Metabolic Pathways database]
* [http://www.worthington-biochem.com/default.html Worthington Biochemical Corporation Enzyme Manual]
* [http://www.worthington-biochem.com/default.html Worthington Biochemical Corporation Enzyme Manual]
⚫
* [http://www.chem.qmul.ac.uk/iubmb/enzyme/ Enzyme Nomenclature]


[[Category:Enzymes]]
[[Category:Enzymes]]

Revision as of 09:33, 3 February 2009

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


Introduction

BRENDA is an electronic information ressource that comprises molecular and biochemical information on enzymes which 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. Here, 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 also improvements of the user interface are incorporated into the BRENDA database.

The latest update was performed in January 2009.

Content and Features

Database:

The database contains more than 40 data fields with enzyme-specific information on more than 4800 EC numbers that are classified according to the IUBMB. The different data fields cover information on the enzyme´s nomenclature, reaction and specificity, enzyme structure, isolation and preparation, enzyme stability, kinetic parameters such as Km value and turnover number, occurrence and localization, mutants and engineered enzymes, application of enzymes and ligand-related data. The data originates from almost 85,000 different scientific articles. Each enzyme entry is clearly linked to at least one literature reference, its source organism and, where available, to the protein sequence of the enzyme[1]. Furthermore, cross-references to external information resources such as sequence and 3D-structure databases as well as biomedical ontologies are provided.

Extensions:

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

Data access:

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

  • Several different query forms (e.g. quick and advanced search)
  • [[SOAP]| SOAP-Interface]
  • EC-tree browser
  • Taxonomy-tree browser
  • Chemical substructure search engine for ligand structures
  • Ontologies for different data fields
  • Thesaurus for ligand names

Availability

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

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:

References

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

Further reading

  • 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  • Schomburg I, Chang A, Schomburg D (2002). "BRENDA, enzyme data and metabolic information". Nucleic Acids Res. 30: 47–49. {{cite journal}}: External link in |title= (help)CS1 maint: multiple names: authors list (link)
  • 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. {{cite journal}}: External link in |title= (help)CS1 maint: multiple names: authors list (link)
  • Pharkya P, Nikolaev EV, Maranas CD (2003). "Review of the BRENDA Database". Metab Eng. 5 (2): 71–73. {{cite journal}}: External link in |title= (help)CS1 maint: multiple names: authors list (link)
  • 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): D431-3. {{cite journal}}: External link in |title= (help)CS1 maint: multiple names: authors list (link)
  • Schomburg D, Schomburg I, Chang A (2006). Springer Handbook of Enzymes (2nd ed.). Heidelberg: Springer.{{cite book}}: CS1 maint: multiple names: authors list (link)
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