title: Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order.
abstract: BACKGROUND
  Drug discovery and design are important research fields in bioinformatics. Enumeration of chemical compounds is essential not only for the purpose, but also for analysis of chemical space and structure elucidation. In our previous study, we developed enumeration methods BfsSimEnum and BfsMulEnum for tree-like chemical compounds using a tree-structure to represent a chemical compound, which is limited to acyclic chemical compounds only.
  
  
  RESULTS
  In this paper, we extend the methods, and develop BfsBenNaphEnum that can enumerate tree-like chemical compounds containing benzene rings and naphthalene rings, which include benzene isomers and naphthalene isomers such as ortho, meta, and para, by treating a benzene ring as an atom with valence six, instead of a ring of six carbon atoms, and treating a naphthalene ring as two benzene rings having a special bond. We compare our method with MOLGEN 5.0, which is a well-known general purpose structure generator, to enumerate chemical structures from a set of chemical formulas in terms of the number of enumerated structures and the computational time. The result suggests that our proposed method can reduce the computational time efficiently.
  
  
  CONCLUSIONS
  We propose the enumeration method BfsBenNaphEnum for tree-like chemical compounds containing benzene rings and naphthalene rings as cyclic structures. BfsBenNaphEnum was from 50 times to 5,000,000 times faster than MOLGEN 5.0 for instances with 8 to 14 carbon atoms in our experiments.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Gokasho, Japan.
authors.forename: Jira
authors.initials: J
authors.lastname: Jindalertudomdee
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Gokasho, Japan. morihiro@kuicr.kyoto-u.ac.jp.
authors.forename: Morihiro
authors.initials: M
authors.lastname: Hayashida
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Gokasho, Japan.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Gokasho, Japan. takutsu@kuicr.kyoto-u.ac.jp.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Akutsu
mesh_terms: D000465:Algorithms; D001554:Benzene / Q000737:chemistry*; D002626:Chemistry, Pharmaceutical / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D009281:Naphthalenes / Q000737:chemistry*; D013237:Stereoisomerism
chemical_list: D009281:Naphthalenes; C031721:naphthalene; D001554:Benzene