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The Biochemical Pathways database (BioPath) contains data 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 warehousing and retrieval system C@ROL (BioPath.Explore). |
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BioPath Contents |
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| 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, C@ROL 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
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C@ROL Features and Benefits
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| standard chemoinformatics search features |
users can easily apply their knowledge about searching chemoinformatic databases by performing full- or substructure searches, property or reaction searches |
| web-based |
no further client installation is required |
| 3D substructure and conformation search |
perform pharmacophore searching quickly without the need of applying a specialized system |
| precursor search |
find starting materials without searching in a reaction database |
| combined searching |
define a query in a natural way without being limited in they way you want to search the data |
| hyperlinks |
conveniently switch between the various areas of information and generate knowledge by bringing information into context |
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Key Features
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- 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
- Annotation of atom-atom mapping numbers
- Application area: tracing of isotopic labeling
- Example: numbers at the element symbols
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Additional Info |
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| Downloadable PDFs
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