BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

By I. Schomburg, Antje Chang, S. Placzek, C. Söhngen, M. Rother, Maren Lang, Cornelia Munaretto, Susanne Ulas, M. Stelzer, A. Grote and 2 more. Nucleic Acids Res., 2012

440 citations recorded by the source corpus.

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme portal (http://www.brenda-enzymes.org) is the main information system of functional biochemical and molecular enzyme data and provides access to seven interconnected databases. BRENDA contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910 000 new EC number–disease relations in more than 510 000 references from automatic search and a classification of enzyme–disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalysed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models.

Subfields: Biotechnology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/db28196d765d2b6d6383df74b60cb67fbcdc1db3

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Citations in the corpus

Data integration in the era of omics: current and future challenges (2014, background): “Moreover, it is possible to complement such information with enzyme kinetics data from databases such as BRENDA [10].”
BRENDA in 2019: a European ELIXIR core data resource (2018, background): “6 million references including information on enzyme/diseases, organisms/tissues, cellular and subcellular localization and kinetic values (3,4).”
Large-Scale Determination of Sequence, Structure, and Function Relationships in Cytosolic Glutathione Transferases across the Biosphere (2014, methodology): “Also, the manually curated databases of biochemical reactions BRENDA [45] and SABIO-RK [46] were mined for data corresponding to the following GST-relevant E.C. numbers: 2.5.1.18, 4.5.1.3, 5.3.99.2, 1.8.5.1, 1.11.1.9, 5.2.1.2, 5.2.1.4, 1.20.4.2, and 1.5.4.1.”
BRENDA in 2015: exciting developments in its 25th year of existence (2014, background): “Furthermore, BRENDA includes large amounts of information on the occurrence of enzymes in organisms, their cellular localization, their involvement in human diseases, their active centers and interfaces, as well as additional kinetic data, resulting from text mining and analysis methods and bioinfor”
Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints (2017, methodology): “Although it has recently been shown that there is a good correlation between in vitro kcat measurements from BRENDA and in vivo values inferred from omics data (Davidi et al, 2016), the future use of this model for specific purposes such as flux prediction of a given pathway should always involve a ”