Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming

Journal of Chemical Information and Modeling

Volumn 51, Issue 11, 2011, Pages 2788-2807

  Imada, Tomoki ^a   Ota, Shunsuke ^a   Nagamochi, Hiroshi ^a   Akutsu, Tatsuya ^b  

^a KYOTO UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; CARBON; GRAPH STRUCTURES; GRAPHIC METHODS; INFORMATION DISSEMINATION; ISOMERS; STEREOCHEMISTRY;

CHEMICAL GRAPHS; GRAPHICAL STRUCTURES; MOLECULAR DESIGN; NITROGEN ATOM; NON-REDUNDANT; OUTERPLANAR GRAPH; STRUCTURAL CENTERS; STRUCTURE ELUCIDATION;

DYNAMIC PROGRAMMING;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL MODEL; CHEMICAL STRUCTURE; DRUG DESIGN; METHODOLOGY; STATISTICS; STEREOISOMERISM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DRUG DESIGN; MODELS, CHEMICAL; MOLECULAR STRUCTURE; STEREOISOMERISM;

EID: 82355182465     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200084b     Document Type: Article

References (25)

1. Cayley, A. On the Mathematical Theory of Isomers Philos. Mag. 1874, 47, 444-446
2. Pólya, G. Kombinatorische Anzahlbestimmungen für Gruppen, Graphen, und chemische Verbindungen Acta Math. 1937, 68, 145-254
3. Faulon, J.-L.; Visco, D. P., Jr.; Roe, D. Enumerating Molecules Rev. Comput. Chem. 2005, 21, 209-286 (Pubitemid 44578719)
4. Gugisch, R.; Rücker, C. Unified Generation of Conformations, Conformers, and Stereoisomers: A Discrete Mathematics-based Approach MATCH Commun. Math. Comput. Chem. 2009, 61, 117-148
5. Mislow, K.; Siegel, J. Stereoisomerism and Local Chirality J. Am. Chem. Soc. 1984, 106, 3319-3328
6. O'Loane, J. K. Optical Activity in Small Molecules, Nonenantiomorphous Crystals, and Nematic Liquid Crystals Chem. Rev. 1980, 80, 41-61
7. Abe, H.; Hayasaka, H.; Miyashita, Y.; Sasaki, S. Generation of Stereoisomeric Structures Using Topological Information Alone J. Chem. Inf. Comput. Sci. 1984, 24, 216-219
8. Contreras, M. L.; Alvarez, J.; Guajardo, D.; Rozas, R. Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation J. Chem. Inf. Model. 2006, 46, 2288-2298 (Pubitemid 46008102)
9. Wieland, T.; Kerber, A.; Laue, R. Principles of the Generation of Constitutional and Configurational Isomers J. Chem. Inf. Comput. Sci. 1996, 36, 413-419 (Pubitemid 126539339)
10. Nourse, J. G. The Configuration Symmetry Group and Its Application to Stereoisomer Generation, Specification, and Enumeration J. Am. Chem. Soc. 1979, 101, 1210-1216
11. Dress, A.; Dreiding, A.; Haegi, H. Classification of Mobile Molecule by Category Theory Stud. Phys. Theor. Chem. 1983, 23, 39-58
12. Tratch, S. S.; Molchanova, M. S.; Zefirov, N. S. A Unified Approach to Characterization of Molecular Composition, Connectivity, and Configuration: Symmetry, Chirality, and Generation Problems for the Corresponding Combinatorial Objects MATCH Commun. Math. Comput. Chem. 2009, 61, 217-266
13. Rücker, C.; Gugisch, R.; Kerber, A. Manual Construction and Mathematics- and Computer-Aided Counting of Stereoisomers. The Example of Oligoinositols J. Chem. Inf. Comput. Sci. 2004, 44, 1654-1665
14. Imada, T.; Ota, S.; Nagamochi, H.; Akutsu, T. Efficient Enumeration of Stereoisomers of Tree Structured Molecules Using Dynamic Programming J. Math. Chem. 2011, 49, 910-970
15. Mitchell, S. L. Linear Algorithms to Recognize Outerplanar and Maximal Outerplanar Graphs Inform. Proc. Lett. 1979, 9, 229-232
16. Horvath, T.; Akutsu, T.; Wrobel, S. A Refinement Operator for Outerplanar Graphs. In Proceedings of the 16th International Conference of Inductive Logic Programming, Technical Report; University of Coruna: Coruna, Spain, 2006; pp 95-97.
17. Rücker, C.; Meringer, M. How Many Organic Compounds are Graph-Theoretically Nonplanar ? MATCH Commun. Math. Comput. Chem. 2002, 45, 153-172
18. Imada, T. Enumeration of Stereoisomers of Outerplanar Chemical Graphs Using Dynamic Programming, Master Thesis; Graduate School of Informatics, Kyoto University: Kyoto, Japan; February 10, 2011.
19. Aho, A. V.; Hopcraft, J. E.; Ullman, J. D. The Design and Analysis of Computer Algorithms; Addison-Wesley: Reading, MA, 1974.
20. Burnside, W. Theory of Groups of Finite Order; Cambridge University Press: Cambridge, U.K., 1897.
21. Jordan, C. Sur Les Assemblages De Lignes J. Reine Angew. Math. 1869, 70, 185-190
22. Imada, T.; Nagamochi, H. Indexing All Rooted Subgraphs of a Rooted Graph, Technical Report 2011-02; Graduate School of Informatics, Kyoto University: Kyoto, Japan, 2011; http://www-or.amp.i.kyoto-u.ac.jp/members/nag/Technical- report/TR2011-002.pdf.
23. Manning, J.; Atallah, M. J. Fast Detection and Display of Symmetry in Outerplanar Graphs Discrete Appl. Math. 1992, 39, 13-35
24. Razinger, M.; Balasubramanian, K.; Perdih, M.; Munk, M. E. Stereoisomer Generation in Computer-Enhanced Structure Elucidation J. Chem. Inf. Comput. Sci. 1993, 33, 812-825
25. Kanehisa, M.; Goto, S.; Furumichi, M.; Tanabe, M.; Hirakawa, M. KEGG for Representation and Analysis of Molecular Networks Involving Diseases and Drugs Nucleic Acids Res. 2010, 38, D335-D360