Service Communautaire d'Information sur la Recherche et le Développement - CORDIS

BIOPATH database

Within WorkPackage 9.6 the work on access to reaction mechanisms (De23) and interface to metabolic pathways (De24) was done with Partner 23. Professor Gasteiger's group have taken the famous Biochemical Pathways wall chart from Roche Applied Science and converted this into a reaction database prior to TEMBLOR and a web based retrieval system called C@ROL was interfaced to this BioPath database. TEMBLOR contributed to enhancing the wide variety of search methods for chemical structures, enzymes, and reactions that can allow one to explore the endogenous metabolism of different species.

Major features of this database are that each molecule is represented by lists of all atoms and bonds (as connection tables), and in the reactions the reaction centres, the atoms and bonds directly involved in the bond rearrangement process, are marked. The information in the database has been enriched by a set of diverse 3D structure conformations generated by the programs CORINA and ROTATE.

The database is accessible on the Internet at:
http://www2.chemie.uni-erlangen.de/services/biopath/index.html
and http://www.mol-net.de/databases/biopath.html
(see also http://www.mol-net.de/software/carol/index.html).

The information in this database can be used to explore enzyme inhibitors as transition state mimics. Furthermore, it was shown how the classification of biochemical reactions based on physicochemical effects at the reaction site, corresponds with the classification of enzymes by the EC code. (see Reitz,M., Sacher,O., Tarkhov,A., Trumbach,D. & Gasteiger,J. Enabling the exploration of biochemical pathways. Org. Biomol. Chem. 2, 3226-3237 (2004). The current system covers prokaryotes, plants, yeasts, animals, over all pathways, with 2175 Biochemical Transformations.

Reported by

University of Erlangen-Nuremberg
Computer Chemistry Center, Nagelsbachstr. 25
91052 ERLANGEN
Germany
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