Biochemical Pathways (BioPath)

The Biochemical Pathways Wall Chart and the corresponding Atlas by G. Michal have been converted into a molecule and reaction database. 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 centers, 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.

For a detailed description please refer to a publication on our Biochemical Pathways database:
Reitz,M., Sacher,O., Tarkhov,A., Trümbach,D. & Gasteiger,J. Enabling the exploration of biochemical pathways. Org. Biomol. Chem. 2, 3226-3237 (2004).

Main Features of BioPath:
Biochemical Transformations
Covered Organisms
prokaryotes, plants, yeasts, animals, overall pathways
subcellular localization of pathways including: cytosol, chloroplasts, mitochondria, endoplasmatic reticulum, peroxysomes, endothelium of blood vessels, vascular muscle cell, extracellular matrix, nucleus, cell membrane, plant cell wall
  • all reactions are stoichiometrically balanced
  • all structures stored as connection tables
  • reaction centers are marked (bonds broken, made or altered during the reaction)
  • atom-atom mapping between starting material and product
  • links to corresponding chart-segment on ExPASy server
  • links to BRENDA entry for each enzyme
  • 3D structures and conformations for each molecule by CORINA and ROTATE

BioPath can be tested online here.

For commercial purposes, BioPath is available from our partner Molecular Networks GmbH.

Financial support for this project was given by the Bundesministerium fuer Bildung und Forschung (bmb+f) (projects no. 08 C 5850 0,08 C 5879, 031U112D, 031U212D, 031U112A and 031U212A).

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