Universität zu Köln, Institut für Biochemie
Zülpicher Straße 47,
50674 Köln, Germany
Phone: (+221) 470-6440,
Fax: (+221) 470-5092
e-mail:D.Schomburg@uni-koeln.de
(www.BRENDA.uni-koeln.de)
With the ongoing development and progress on structural and functional genomics it is becoming more essential to collect and access metabolic information of gene products. BRENDA (BRaunschweiger ENzyme DAtabase), the most complete information system on enzymes at present, has been developed to provide a tool in the field of bioinformatics to understand biological functions and the biochemistry of the cell. Thus the retrieval of functional parameters, suitable data collections and genome information is a prerequisite for the simulation and construction of whole metabolic paths and networks.
BRENDA contains information on biochemical and molecular properties of all those enzymes that have been assigned to an EC number by the IUBMB (International Union of Biochemistry and Molecular Biology). The database covers information on enzyme nomenclature, occurrence, catalyzed reaction, substrates/products, inhibitors, cofactors, activators, structure, and stability. All data and information are manually extracted and evaluated from the primary literature by scientists.
BRENDA is accessible to the academic community at www.brenda.uni-koeln.de. Commercial users need a license available at www.science-factory.com
The number of literature references is increasing quickly, therefore we started to use automatic information extraction techniques, tested for the inclusion of medical information, i.e. disease-related publications. The references in electronic format were taken from the PubMed database, parsed for relevant keyphrases and associated with the correlated enzymes. Presently information on 789 enzymes and their associated human diseases has been included into BRENDA.
Additionally, the OMIM database (Online Mendelian Inheritance in Men) was parsed for enzyme information correlated to human genes and genetic disorders. So far 630 EC numbers could be linked to 2100 OMIM entries.
A major part in the BRENDA database are the chemical compounds, functioning as ligands in the interaction with enzymes. More than 33.000 different ligands with altogether 320.000 enzyme/ligand relationships are stored in the database. These enzyme-ligand interactions are described in the information fields, i.e. natural or in vitro substrates, inhibitors, activating compounds, cofactors, bound metals etc.. In BRENDA the ligands are stored as compound names, SMILES strings (Simplified Molecular Input Line Entry Specification) and Molfiles. The two latter forms are interchangeable with respect to the connectivity information and allow substructure searches. Presently connectivity information on 23.000 of these ligands are included in BRENDA. Additionally the chemical structure of these compounds can be displayed as images.