Objective
The main objective of this project is to bring to the public domain, using modern internet protocols, BRENDA, the most complete existing collection of experimental data on enzyme physical-chemical and functional properties, and to integrate it with other key available databases containing information on genome and protein sequences, on tissue and cellular location, and organisms. Another important objective of this project is to include in this system additional, not readily available information. This information pertains to the detailed characteristics of the molecular interactions in 3D structures of enzyme-ligand complexes, and of enzyme active sites, and to detailed structural and chemical descriptions of the small molecules (substrates, inhibitors, effectors) that interact with each enzyme.
BRENDA has been developed by partner 1 (Schomburg), first at the German National Centre of Biotechnology in Braunschweig and now at Cologne University. It includes information on all enzymes classified to date(see appendix 2, 2.7 for a typical data set on one enzyme); it is presently held in a pseudo-relational database system in house and is available only in printed form (see references).
In order to make this available via the internet, the present data has to be split into molecule-specific information that is directly connected with enzyme sequence and 3D-structure data. In the present form, the data bank has links to the sequence data banks and PDB but the information is integrated under the umbrella of the EC-number (EnzymeCommission number) with an indirect link to the individual enzyme via literature references. This assignment and verification of the current enzyme data in relation to individual organisms/tissues and establishing procedures for its continued up-dating and relationship to the needs of other international bodies will be performed by partners 1, (Cologne), in cooperation with partners 3 and 4 (Dublin and Cambridge). The integration of BRENDA with other key databases and information will be performed using the internet based 'database integration engine' SRS developed and maintained by partner 3 (EBI).
Whenever structural data about specific enzymes, and enzyme-ligand complexes are available in the protein Data Bank (PDB), detailed characteristics of the inter-molecule interactions in these complexes will be derived from specialized surveys and analyses, by partner 2 (Brussels), and integrated with the experimental and sequence information. For all substrates, products, inhibitors, etc. the chemical and structural descriptions in the form of SMILES strings will be provided by partner 4(Glaxo), and also integrated.
The deliverable of this project will be a highly valuable data resource on enzyme function integrated with a large number of other existing data collections, as well as with structural and chemical data on small molecules and on enzyme-ligand complexes. The integrated resource will be-accessible to the scientific community via the SRS system.
The project complies with the aims described in the Biotechnology objectives description, as described in area 8.1: "Information infrastructures" as: integration of new emerging databases, unique access points to sets of related information sources. It also has close connections to area 1.1: "Biological Components of Cell Factories", where "enzymes mechanisms of activity and control, inhibitors, post-translational events are mentioned. With respect to the planned addition of structure-related information another close link is given to area 6.1: "Structure-function relationship", in particular 6.1.3: "Biomolecules with the desired functions."
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques.
- natural sciencescomputer and information sciencesdatabases
- natural sciencescomputer and information sciencesinternetinternet protocols
- natural sciencesbiological sciencesgeneticsgenomes
- natural sciencesbiological sciencesbiochemistrybiomoleculesproteinsenzymes
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Call for proposal
Data not availableFunding Scheme
CSC - Cost-sharing contractsCoordinator
50674 KOELN
Germany