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. 2011 Jan;39(Database issue):D670-6.
doi: 10.1093/nar/gkq1089. Epub 2010 Nov 9.

BRENDA, the enzyme information system in 2011

Maurice Scheer  1 , Andreas Grote, Antje Chang, Ida Schomburg, Cornelia Munaretto, Michael Rother, Carola Söhngen, Michael Stelzer, Juliane Thiele, Dietmar Schomburg
Affiliations

BRENDA, the enzyme information system in 2011

Maurice Scheer et al. Nucleic Acids Res. 2011 Jan.

Abstract

The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information system is the main collection of enzyme functional and property data for the scientific community. The majority of the data are manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. The number of manually annotated references increased by 30% to more than 100,000, the number of ligand structures by 45% to almost 100,000. New query, analysis and data management tools were implemented to improve data processing, data presentation, data input and data access. BRENDA now provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models.

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Figures

Figure 1.
Figure 1.
(a) Access to the new ligand search form from the BRENDA homepage and (b) The new ligand search form. As an example the search results for all ligand names starting with ‘protoporphyrin’ are shown.
Figure 2.
Figure 2.
The Ligand Summary Page displays the complete information for any ligand stored in BRENDA. As an example, the first part of the site for protoporphyrin IX is shown (http://www.brenda-enzymes.org/php/ligand_flatfile.php4?brenda_ligand_id=15923). On the upper right, the blue arrow points to an enlarged view of the navigation bar which provides hyperlinks for the direct access to the different information fields.
Figure 3.
Figure 3.
Visualization of dihydrolipoyl dehydrogenase with marked nucleotide phosphate-binding region.
Figure 4.
Figure 4.
Distribution of the temperature optimum for all Archaea enzymes in BRENDA.
Figure 5.
Figure 5.
Link to the SBML tool within the BRENDA main menu (SBML button on left panel).
See this image and copyright information in PMC

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References

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