BioPath - Database on Biochemical Pathways

Overview [hide]
  1. Features & Functionality
  2. Key Features
  3. Additional Info
  4. Online Demonstration

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.

BioPath provides access to biological transformations and regulations as described on the "Biochemical Pathways" chart. The BioPath database is available in MDL 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 1,175 (online version)
2,074 (commercial version)
Biochemical transformations 1,545 (online version)
2,881 (commercial version)
Covered organisms Prokaryotes, plants, yeasts and animals, general pathways
Additonal 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 MDL MOL/RDFile format, BioPath.Explore proprietary database
Features
  • All structures are available as connection tables
  • Reaction centers and bonds broken and made in a reaction have been marked
  • All atoms have been mapped between starting materials and products
  • Enzymes are represented by their names and the EC code number
  • All compounds and reactions are marked with their corresponding chart coordinates
  • 3D structures and conformations have been added using CORINA and ROTATE

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 and BioPath.Explore - Biochemical Pathways Database

Online Demonstration

Version 1 of BioPath and BioPath.Explore can be tested free of charge online.