Our primary goal in the development of RCLASS is to extend the EC classification so that it also covers putative reactions that are not yet well characterized. High-throughput measurement techniques hint at the existence of considerable numbers of orphan metabolites, i.e., compounds that are known to be present in living organisms but whose synthetic/degradation pathways are unknown ( Kotera et al., 2008). In order to identify the enzyme proteins involved in these pathways, it is essential to characterize or classify the putative reaction equations that are often incomplete. In principle, the official EC numbers cannot

be used for this purpose because their assignment requires confirmed experimental evidence of enzyme activity and a complete selleckchem reaction equation. In order to describe the relationships between putative reactions and putative enzyme proteins (or genes), it is PDGFR inhibitor essential to develop an enzyme classification scheme that is applicable not only for the confirmed reactions with complete equations, but also for the putative reactions, even if the equations are incomplete. Finding possible enzyme reactions from metabolomic data naturally starts with a pair of compounds (which we refer to as a “reactant pair”)

corresponding to a reaction equation, not always a complete reaction equation (Kotera et al., 2004). Possible chemical transformation within the compounds can be obtained by comparing the

two chemical structures. Technically, chemical compounds are represented as graph structures, where the edges represent chemical bonds, and the nodes represent atoms attached with functional group information. In order to distinguish functional groups and microenvironments of atoms, five atom species (C, N, O, S and P) are classified into the 68 Farnesyltransferase KEGG atom types (Hattori et al., 2003) (such as “N1a” for an amino group in Figure 1). As a result of graph comparison, the matched subgraph corresponds to the conserved atom group under the enzymatic reaction, and the unmatched sub-graph of each compound corresponds to the eliminated or the added atom groups. The boundary area between the conserved and the non-conserved sub-graphs can be regarded as the reaction center on which the putative enzyme acts. In such a way, the RDM chemical transformation patterns are extracted from a reactant pair in the computational manner (Kotera et al., 2004 and Hattori and Kotera, 2011). The RDM pattern is represented with a string of the KEGG Atom Types, and describes a chemical bond that is generated or eliminated in a reaction. We defined the RCLASS entries that represent a set of chemical transformations found in a Substrate–product pair (reactant pair). Each RCLASS entry was given identification numbers (RC numbers). An RCLASS entry may consist of multiple RDM patterns when more than one chemical bond is generated or eliminated.