RPAIR: A Database of Chemical Transformation Patterns in Enzymatic Reactions

Chemical genomics is the next stage of post-genomic analysis. Drugs, environmental substances and various chemical compounds contribute to the fluctuation of bio-systems. Therefore, chemical genomic analysis would require the investigation of relationships between genomes and their extracellular environments. These relationships between bio-systems and environments include complicated biochemical reactions. At present, biochemical reactions are hierarchically classified using EC (Enzyme Commission) numbers [1]. However, the classification is not totally based on chemical reactions, but also includes enzymes or enzyme genes. EC numbers are commonly utilized as identifiers of enzymes or enzyme genes [4]. In order to expand our current limited knowledge on biochemical reactions as represented by EC numbers, we developed a novel database that provides the patterns of the conformational changes between the chemical structures of the substrate and product. This database is integrated into the KEGG resource [3], so other databases in KEGG have links to the entries of this database. All of the data is available from http://www.genome.jp/reaction/.