While a number of genomes from different organisms is available worldwide now and the scientific community is awaiting the conclusion of the project to sequence the first mammalian genome the scientific focus is more and more turned to functional genomics. In the field of bioinformatics this involves the identification of functions and structures from genome information, development of suitable data formats, data standards and data collections for functional information and the simulation of molecular interactions from the atomic level to the simulation of whole metabolic and finally signal regulatory metabolic paths and networks.
An urgently needed prerequisite for this whole new scientific approach, characterized by a holistic
view on the biochemistry of the cell, is the existence of suitable information systems that deliver
the parameters for the simulations and include the information to reconstruct paths and networks.
For the metabolic part of this network BRENDA represents the most comprehensive data system
available worldwide. Having emerged from a series of books, the Enzyme Handbooks, published
by Springer, Heidelberg BRENDA has now been integrated into a relational database system and
is available via the databaseintegration tool SRS on the web. It can be accessed at
http:srs.ebi.ac.uk and www.brenda.unikoeln.de brenda.
It is the most complete information system on enzymes at present, containing information on all those enzymes that have been assigned an EC Number by the IUBMB (International Union of Biochemistry and Molecular Biology). All entries and data are literaturebased. Presently it contains 3636 enzymes in 6 classes.
Information from the areas nomenclature, reaction and specificity, structure, organism, stability, references and links is included in BRENDA. In order to allow the automatic organismspecific construction of metabolic networks the datastructure was recently changed fundamentally by adding the corresponding organism to each value and information. Now each entry consists of the actual parameter, the literature reference, a commentary, and the organist information.
With this new format BRENDA offers new possibilities:
Direct links are established via SRS to a large number of data bases. Direct links from BRENDA to the NCBI Taxonomy browser and to Medline are being included.
BRENDA now also offers the possibility of direct author input. Published data can be submitted for all enzymes, with or without a known EC Number. As a cooperation project within the framework of the German Human Genome Project links to expression information and medical information will be integrated thereby enabling BRENDA to be a direct link between genotype and phenotype.
Availability: BRENDA is available for nonprofit research free of charge. Companies are required to aquire a license. Inhouse versions including relational data base systems are available.