BRENDA, the enzyme information system in 2011

By M. Scheer, A. Grote, Antje Chang, I. Schomburg, Cornelia Munaretto, M. Rother, C. Söhngen, M. Stelzer, J. Thiele, Dietmar Schomburg. 2010

422 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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In Molecular Biology

1. Linda J. Broadbelt
2. Bernhard O. Palsson

Citations in the corpus

• Efficient searching and annotation of metabolic networks using chemical similarity (2015, methodology): “Algorithmically, this is difficult to account for because the ensemble of BRENDA entries searched is tied to the biotransformations used by the putative network-generating software, but errors are rare in the highest-scoring results and can easily be identified by inspection when they occur.”