BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

By Antje Chang, M. Scheer, A. Grote, I. Schomburg, Dietmar Schomburg. Nucleic Acids Res., 2008

475 citations recorded by the source corpus.

The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system containing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calculating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. The data in BRENDA are manually curated from more than 79 000 primary literature references. Each entry is clearly linked to a literature reference, the origin organism and, where available, to the protein sequence of the enzyme protein. A new search option provides the access to protein-specific data. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are additional databases created by continuously improved text-mining procedures. These databases ought to provide a complete survey on enzyme data of the literature collection of PubMed. The web service via a SOAP (Simple Object Access Protocol) interface for access to the BRENDA data has been further enhanced.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/5c70093889dc6520efc85e6c3132b33da7079cd3

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Citations in the corpus

Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs (2013, background): “Other questions may be answered as more microbial genomes are fully sequenced, and through increased representation of organisms derived from the environment in existing databases of organisms and enzymes (e.g. Cantarel et al. 2008; Chang et al. 2009).”
BRENDA, the enzyme information system in 2011 (2010, background): “Since the last publication in 2009 (2) the data content has increased substantially, and new tools and functionalities for the query and data analysis were implemented.”
Uberon, an integrative multi-species anatomy ontology (2012, background): “The closest has been the Brenda Tissue Ontology (BTO) [22], a terminology applicable across plants, fungi and animals, including gross anatomy, as well as cell types and diseases.”
Chemical Entities of Biological Interest: an update (2009, methodology): “Additional cross-references to patent data as well as to resources such as BRENDA and NMRShiftDB have allowed users to use ChEBI as a chemistry portal to other resources.”
IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding (2009, methodology): “Experimental data (IC50 values) and accompanying assay information were manually extracted from primary literature results and other relevant databases: JCVIPathema-Clostridium (13), Brenda (14) and Protein Data Bank (15).”
Alteration of enzyme specificity by computational loop remodeling and design (2009, background): “We consider hGDA to be the best starting point for such an effort based on the complement of deaminases that exist in the human genome (23, 24).”
MODOMICS: a database of RNA modification pathways. 2008 update (2008, background): “as KEGG (17) or enzyme databases such as BRENDA (18), in order to allow both a generic view on the systems biology of RNA, and detailed information on its components.”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, background): “In order to determine which metabolites are preferentially recognized by enzymes, processing the literature or browsing information collected in enzyme databases such as BRENDA (Barthelmes et al., 2007) is often necessary.”