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Our continuing tour of free chemistry databases and Web services takes us today to the Biochemical Pathways Database (BioPath), a structure-searchable compilation of biochemical pathways. From the about page:

BioPath contains a library of cross-linked biochemical molecules and reactions. All structure and reaction information is stored on an atomic level allowing the direct access to all atoms and bonds of all metabolites and to the bonds broken and made during an enzymatic reaction.

BioPath is designed to support scientists to understand the impact of gene regulations on biological systems for drug target identification and provides the following features:

• 1,175 molecules with connection tables including stereochemical information
• 1,545 biochemical reactions stoichiometrically balanced, with marked reaction centers and atom-atom mapping numbers between educts and products
• 1,000 unique enzymes represented by names and EC numbers
• 202 pathways represented by names
• Covered organism: prokaryotes, plants, yeasts and animals, general pathways
• Subcellular localization of pathways (cytosol, chloroplasts, mitochondria, ...)

BioPath consists of a network of reactions of small molecules mediated by enzymes. Both individual molecules and their transformations can be searched by structure using an in-page editor. Each search mode is accessed by clicking on the buttons labeled "Start Structure-Based Search" or "Start Reaction-Based Search" buttons, respectively.

Starting a structure-based search opens a pop-up window in which molecules can be searched by a number of parameters including atom count, hydrogen-bond donors, and number of rotatable bonds. For example, drawing the structure of naphthalene and clicking search displays a hit list page giving three hits. Clicking on the hyperlinked numerical identifier pulls up the structure summary page for the matching molecule. This page contains summary information, but more interestingly it also contains information about the pathways in which the molecule participates.

Each small molecule contained in by a path is linked to a reaction and to a grid square in the Roche Applied Bioscience "Biochemical Pathways" wall chart. Clicking on a reaction link displays the small molecule transformation along with information on reactant and product. Clicking on a grid square info link displays a magnified view of the Roche poster in which the small molecule appears.

Reaction search works similarly to structure search, except that the structure editor accepts a reactant and a product. Reaction searching, although giving correct results, was somewhat limited in constraining searches to reactions at a particular atom. For example, searching for the transformation of substituted benzenes into phenols via oxidation resulted in many hits in which a benzene carbon was not oxidized. The online documentation suggests that the way to remedy this problem is to include atom labels on reactant and product, but in my hands this feature did not work.

BioPath offers a good example of how existing data sources can be transformed into useful Web applications. Although not perfect, the overall design and implementation worked well enough to be useful. For anyone interested in biochemical pathways and the small molecules participating in them, BioPath makes an excellent resource.

Kudos

• Easy-to-use query and search interfaces.
• Numerous structure search options.
• Repurposing existing resources for the Web.

Ideas for Improvement

• Reliable reaction atom mapping.
• Eliminate popup windows for better workflow.
• Make the Roche wall chart itself a clickable image map that links to a database pathway or molecule.