Web Site Review
Review of the BRENDA Database
Introduction
The rapid sequencing of a large number of genomes has made it imperative to organize the available data in ways that facilitate easy analysis. BRENDA (BRaunschweig ENzyme DAtabase) was created in 1987 at the German National Research Center for Biotechnology at Braunschweig and is currently being maintained at the University of Cologne. As of February 2003, it provides information on 40,000 different enzymes represented by 4,087 EC numbers, and present in more than 9000 different organisms as of February, 2003 (Schomburg et al., 2002a). The database is accessible at no charge at http://www.brenda.unikoeln.de for academic purposes.
Section snippets
The contents
The enzyme content of BRENDA can be accessed using the enzyme EC number, the enzyme name and the organism name. A search can also be conducted based on either the taxonomy tree of the organism in which the enzyme is present or the EC tree of the enzyme. The last classification categorizes enzymes into six different classes based on their functions. An advanced search can be performed for a combination of two fields, for instance, all enzymes which have glucose as their natural substrate and are
Strengths and weaknesses
The BRENDA webpage provides a simple and user-friendly interface. The homepage lists all the fields for which information can be obtained on an enzyme. Each field is accessible directly from this page making it easy for the reader to navigate the website. BRENDA is quite comprehensive in terms of both the number of enzymes included in the database and the broad range of properties on which information about an enzyme can be extracted. It also enables a user to get all the data compiled from
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Cited by (37)
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Virtual screening: An in silico tool for interlacing the chemical universe with the proteome
2015, MethodsCitation Excerpt :For developing more reliable scoring functions, curated test sets of binding data (preferentially Kd values) complemented with microcalorimetric data are increasingly used. Databases comprising such test sets are: BRENDA [138–140], BindingDB [141], PDBCal [142], AffinDB [143], BindingMOAD [144,145], PDBbind [146,147], Ligand–Protein Database [148], ProLINT (restricted to phosphatases and kinases) [149] and PLD [150] (containing experimental and calculated binding energies, obtained by a knowledge-based method [151,152]). The PDBCal, the AffinDB, the BindingMOAD, the PDBbind and the Protein–Ligand Database are the most suitable for scoring function development.
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On the importance of reaction networks for synthetic living systems
2019, Emerging Topics in Life Sciences -
An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment
2018, PLoS Computational Biology