Generation of molecular graphs for QSAR studies: An approach based on supergraphs

Journal of Chemical Information and Modeling

Volumn 47, Issue 6, 2007, Pages 2077-2088

  Melnikov, Andrey A ^a   Palyulin, Vladimir A ^a   Zefirov, Nikolai S ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; QUANTUM CHEMISTRY; STOCHASTIC MODELS; STRUCTURE (COMPOSITION);

COMBINATORIAL CHEMISTRY; MOLECULAR GRAPHS; QSAR; STRUCTURAL CONSTRAINTS;

GRAPH THEORY;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

COMPUTATIONAL BIOLOGY; MOLECULAR STRUCTURE; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 37249007674     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700156f     Document Type: Article

References (30)

1. Lindsay, R. K.; Buchanan, B. G.; Feigenbaum, E. A.; Lederberg, J. Applications of artificial intelligence for organic chemistry: The Dendral Project; McGraw-Hill: New York, 1980.
2. Kudo, Y.; Sasaki, S. I. Principle for Exhaustive Enumeration of Unique Structures Consistent with Structural Information. J. Chem. Inf. Comput. Sci. 1976, 16, 43-49.
3. Shelley, C. A.; Hays, T. R.; Munk, M. E.; Roman, R. V. An Approach to Automated Partial Structure Expansion. Anal. Chim. Acta 1978, 103, 121-132.
4. Benecke, C.; Grund, R.; Hohberger, R.; Kerber, A.; Laue, R.; Wieland, T. MOLGEN+, a generator of connectivity isomers and stereoisomers for molecular structure elucidation. Anal. Chim. Acta 1995, 314, 141 -147.
5. Bangov, I. P. Computer-assisted structure generation from a gross formula. 4. Fighting against graph-isomorphism disease. MATCH Commun. Math. Chem. 1992, 27, 3-30.
6. Bohanec, S.; Zupan, J. Structure Generator GEN. MATCH Commun. Math. Chem. 1992, 27, 49-85.
7. Faulon, J. L. Stochastic Generator of Chemical Structure. 1. Application to the Structure Elucidation of Large Molecules. J. Chem. Inf. Comput. Sci. 1994, 34 (5), 1204-1218.
8. Molchanova, M. S.; Shcherbukhin, V. V.; Zefirov, N. S. Computer Generation of Molecular Structures by the SMOG Program. J. Chem. Inf. Comput. Sci. 1996, 36 (4), 888-899.
9. Molodtsov, S. G. The generation of molecular graphs with obligatory, forbidden and desirable fragments. MATCH Commun. Math. Comput. Chem. 1998, 37, 157-162.
10. Luinge, H. J. AEGIS, a Structure Generation Program in Prolog. MATCH Commun. Math. Chem. 1992, 27, 175-189.
11. SYBYL, version 7.0; Tripos Inc.: St. Louis, MO, 2006.
12. Anderson, A. C. The Process of Structure-Based Drug Design. Chem. Biol. 2003, 10, 787-797.
13. Schüller, A.; Schneider, G.; Byvatov, E. SMILIB: Rapid Assembly of Combinatorial Libraries in SMILES Notation. QSAR Comb. Sci. 2003, 22, 719-721.
14. Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
15. Gugisch, R.; Kerber, A.; Laue, R.; Meringer, M.; Weidinger, J. MOLGEN-COMB, a software package for combinatorial chemistry. MATCH Commun. Math. Comput. Chem. 2000, 41, 189-203.
16. 2, version 4.10; Accelrys, Inc.: San Diego, CA, 2005.
17. MOE, version 2006.08; Chemical Computing Group Inc.: Montreal, Canada, 2006.
18. Douguet, D.; Thoreau, E.; Grassy, G. A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm. J. Comput.-Aided Mol. Des. 2000, 14,449-466.
19. Pegg, S.; Haresco, J.; Kuntz, I. A genetic algorithm for structure-based de novo design. J. Comput.-Aided Mol. Des. 2001, 15, 911 -933.
20. Jamois, E.; Lin, C.; Waldman, M. Design of focused and restrained subsets from extremely large virtual libraries. J. Mol. Graphics Modell. 2003, 22, 141-149.
21. Gillet, V.; Willett, P.; Fleming, P.; Green, D. Designing focused libraries using MoSELECT. J. Mol. Graphics Modell. 2002, 20, 491-498.
22. Kubinyi, H. QSAR: Hansch Analysis and Related Approaches; VCH: Weinheim, 1993.
23. Netzeva, T. I.; Worth, A. P.; Aldenberg, T.; Benigni, R.; Cronin, M. T. D.; Gramatica, P.; Jaworska, J. S.; Kahn, S.; Klopman, G.; Marchant, C. A.; Myatt, G.; Nikolova-Jeliazkova, N.; Patlewicz, G. Y.; Perkins, R.; Roberts, D. W.; Schultz, T. W.; Stanton, D. T.; van de Sandt, J. J. M.; Tong, W.; Veith, G.; Yang, C. ECVAM WORKSHOP REPORT Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. ATLA 2005, 33, 155-173.
24. Lomova, O. A.; Sukhachev, D. V.; Kumskov, M. I.; Palyulin, V. A.; Tratch, S. S.; Zefirov, N. S. The Generation of Molecular Graphs for QSAR Studies by the Acyclic Fragment Combining. MATCH Commun. Math. Chem. 1992, 27, 153-174.
25. Tratch, S. S.; Lomova, O. A.; Sukhachev, D. V.; Palyulin, V. A.; Zefirov, N. S. Generation of Molecular Graphs for QSAR Studies: An Approach Based on Acyclic Fragment Combinations. J. Chem. Inf. Comput. Sci. 1992, 32, 130-139.
26. Smith, E. G. The Wiswesser Line-Formula Chemical Notation; McGraw-Hill: New York, 1968.
27. Mel'nikov, A. A.; Palyulin, V. A.; Zefirov, N. S. Generation of Molecular Graphs for QSAR Studies. Dokl. Chem. 2005, 402, 81-85.
28. Palyulin V. A.; Melnikov, A. A.; Zefirov, N. S. An Approach to the Generation of Molecular Graphs for QSAR Studies Based on Supergraphs. Book of Abstracts of 2 German conferences on chemoinformatics, November 12-14, 2006, Goslar, Germany, p 55.
29. MDL CTfile Formats, http://mdli.com/solutions/white_papers/ ctfile_formats.jsp (accessed May 5, 2007).
30. Kerber, A.; Laue, R.; Meringer, M. An Application of the Structure Generator MOLGEN to Patents in Chemistry. MATCH Commun. Math. Comput. Chem. 2003, 47, 169-172.