BioPath - Database on Biochemical Pathways

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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 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

  • Contains about 14,000 chemical structures
  • Contains about 3,900 biochemical transformations (reactions)
  • Covered organisms of prokaryotes, plants, yeasts and animals, general pathways
  • Provides additional information on 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
  • Supports the formats MOL/RDFile and SQLite database
  • Provides the following features
    • Structures available as connection tables
    • Atoms of substrates and products annotated by atom-atom mapping numbers
    • Reaction centers marked for all reactions
    • Enzymes represented by names and EC number
    • 3D coordinates of small molecules generated by CORINA Classic
    • Molecules classified by taxonomy approach
    • New content focuses 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.