Elucidation of Metabolic Pathways from Enzyme Classification Data

The IUBMB
Enzyme List
is widely used by other databases as a source for avoiding ambiguity in the recognition of enzymes as catalytic entities. However, it was not designed for metabolic pathway tracing, which has become increasingly important in systems biology. A
Reactions Database
has been created from the material in the
Enzyme List
to allow reactions to be searched by substrate/product, and pathways to be traced from any selected starting/seed substrate. An extensive synonym glossary allows searches by many of the alternative names, including accepted abbreviations, by which a chemical compound may be known. This database was necessary for the development of the application
Reaction Explorer
( ), which was written in Real Studio ( ) to search the
Reactions Database
and draw metabolic pathways from reactions selected by the user. Having input the name of the starting compound (the “seed”), the user is presented with a list of all reactions containing that compound and then selects the product of interest as the next point on the ensuing graph. The pathway diagram is then generated as the process iterates. A contextual menu is provided, which allows the user: (1) to remove a compound from the graph, along with all associated links; (2) to search the reactions database again for additional reactions involving the compound; (3) to search for the compound within the
Enzyme List
.