Masahiro Hattori (email@example.com)
Yasushi Okuno (firstname.lastname@example.org\smallskip)
Susumu Goto (email@example.com)
Minoru Kanehisa (firstname.lastname@example.org)
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
We have developed an efficient algorithm for comparing two chemical compounds, where the chemical structure is treated as a 2D graph consisting of atoms as vertices and covalent bonds as edges. Based on the concept of functional groups in chemistry, 68 atom types (vertex types) are defined for carbon, nitrogen, oxygen, and other atomic species with different environments, which has enabled detection of biochemically meaningful features. Maximal common subgraphs of two graphs can be found by searching for maximal cliques in the association graph, and we have introduced heuristics to accelerate the clique finding. Our heuristic procedure is controlled by some adjustable parameters. Here we applied our procedure to the latest KEGG/LIGAND database with different sets of parameters, and demonstrated the correlation of parameters in our algorithm with the distribution of similarity scores and/or the execution time. Finally, we showed the effectiveness of our heuristics for compound pairs along metabolic pathways.