BioPath - Database on Biochemical Pathways

BioPath is a database of biochemical pathways that provides access to metabolic transformations and cellular regulations derived from the Roche Applied Science "Biochemical Pathways" wall chart.

In the current version 3 BioPath also provides access to biological transformations reported in the primary literature. The BioPath database is available in Symyx MOL/RDF format for integration into existing retrieval systems or, optionally, fully integrated into the web-based retrieval system BioPath.Explore.

Features & Functionality

Features Description
Structures about 13,000
Biochemical transformations about 3,600
Covered organisms Prokaryotes, plants, yeasts and animals, general pathways
Additional information Subcellular localization of pathways including: cytosol, chloroplasts, mitochondria, endoplasmatic reticulum, peroxysomes, endothelium of blood vessels, vascular muscle cell, animal extracellular matrix, nucleus, animal cell membrane, plant cell wall
Formats Symyx MOL/RDFile format, SQLite database
Features
  • All structures are available as connection tables
  • All atoms of the substrates and products have been annotated by atom-atom mapping numbers
  • The reaction centers have been marked for all reactions
  • Enzymes are represented by their names and the EC number
  • 3D coordinates of small molecules have been added using CORINA
  • Molecules are classified by a taxonomy approach
  • New content is focused on phytochemicals (e.g., carotenoids)

Key Features

  • Mass-balanced reactions
  • Small molecules (e.g., water, protons) that are often not mentioned in reaction equations are included
  • Rate of stoichiometrically balanced reactions in BioPath: 100%
  • Marking of the reaction center
    • Application area: searching on the reaction center (e.g., all C=C building reactions)
    • Example: single blue line: changed bond order; double blue line: make/break bond
      example reaction center
  • Annotation of atom-atom mapping numbers
    • Application area: tracing of isotopic labeling
    • Example: numbers at the element symbols
      example atom-atom mapping numbers

Additional Info

Downloadable PDFs

Slide Show

BioPath - Database on Biochemical Pathways

License

Academic users may use the BioPath website without paying any license fee. Any users intending to use the BioPath database for commercial purposes have to obtain a license.

Online Demonstration

BioPath and BioPath.Explore can be tested free of charge online.