A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules

Journal of Chemical Information and Computer Sciences

Volumn 44, Issue 3, 2004, Pages 1079-1087

  Brown, Nathan ^a   McKay, Ben ^a   Gilardoni, François ^a   Gasteiger, Johann ^b  

^a Avantium Technologies BV   (Netherlands)

^b UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; CHROMOSOMES; CONSTRAINT THEORY; GENETIC ALGORITHMS; GRAPH THEORY; MOLECULES; OPTIMIZATION; PERTURBATION TECHNIQUES; POLYMERS;

COMPUTER-AIDED MOLECULAR DESIGN (CAMD); MOLECULAR FRAGMENTS; MOLECULAR GRAPHS; MUTATION;

COMPUTER AIDED DESIGN;

ALGORITHM; ARTICLE; COMPUTER AIDED DESIGN; EVOLUTION; MUTATION;

ALGORITHMS; COMPUTER-AIDED DESIGN; EVOLUTION; MUTATION;

EID: 2942700379     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci034290p     Document Type: Review

References (38)

1. Willis, R. C. 2001: A Dock Odyssey. Modern Drug Discovery 2001, 4(9), 30-32.
2. Joseph-McCarthy, D. An Overview of In Silico Design and Screening: Toward Efficient Drug Discovery. Current Drug Discovery 2002, March, 20-23.
3. Glen, R. C.; Payne, A. W. R. A Genetic Algorithm for the Automated Generation of Molecules within Constraints. J. Comput.-Aided Mol. Des. 1995, 9, 181-202.
4. Devillers, J. Designing Molecules with Specific Properties from Intercommunicating Hybrid systems. J. Chem. Inf. Comput. Sci. 1996, 36, 1061-1066.
5. Goh, G. K.-M.; Foster, J. A. Evolving Molecules for Drug Design Using Genetic Algorithms via Molecular Trees. In GECCO 2000; Proceedings of the Genetic and Evolutionary Computation Conference; Whitley, D., Goldberg, D. E., Cantu-Paz, E., Spector, L., Parmee, I., Beyer, H.-G., Eds.; Morgan-Kaufmann: San Francisco, CA, 2000; pp 27-33.
6. Pegg, S. C.-H.; Haresco, J. J.; Kuntz, I. D. A Genetic Algorithm for Structure-Based De Novo Design. J Comput.-Aided Mol. Des. 2001, 15, 911-933.
7. Böhm, H.-J. The Computer Program LUDI: A New Method for the De Novo Design of Enzyme Inhibitors. J. Comput.-Aided Mol. Des. 1992, 6, 61-78.
8. Gillet, V.; Johnson, A. P.; Mata, P.; Sike, S.; Williams, P. SPROUT: A Program for Structure Generation. J. Comput.-Aided Mol Des. 1993, 7, 127-153.
9. Nishibata, Y.; Itai, A. Automatic creation of drug candidate structures based on receptor structure. Starting point for artificial lead generation. Tetrahedron 1991, 47, 8985-8990.
10. Rotstein, S. H.; Murcko, M. A. GenStar: A method for de novo drug design. J. Comput.-Aided Mol. Des. 1993, 7, 23-43.
11. Goldberg, D. E. Genetic Algorithms in Search, Optimisation and Machine Learning; Addison-Wesley: Reading, MA, 1989.
12. Evolutionary Algorithms in Computer-Aided Molecular Design; Clark, D. E., Ed.; Wiley-VCH: Weinheim, 2000.
13. Koza, J. R. Genetic Programming; MIT Press: Cambridge, MA, 1992.
14. Harvey, I. Species Adaptation Genetic Algorithms: A Basis for a Continuing SAGA. In Proceedings of the First European Conference on Artificial Life: Toward a Practice of Autonomous Systems; Varela, F. J., Bourgine, P., Eds.; MIT Press/Bradford Books: Cambridge, MA, 1992; pp 346-354.
15. Ferreira, C. Gene Expression Programming: A New Adaptive Algorithm for Solving Problems. Complex Systems 2001, 13, 78-129.
16. Gillet, V. J.; Downs, G. M.; Ling, A. (B.); Lynch, M. F.; Venkataram, P.; Wood, J. V.; Dethlefsen, W. Computer Storage and Retrieval of Generic Chemical Structures in Patents. 8. Reduced Chemical Graphs, and their Application in Generic Chemical Structure Retrieval. J. Chem. Inf. Comput. Sci. 1987, 27, 126-137.
17. Rarey, M.; Dixon, J. S. Feature Trees: A New Molecular Similarity Measure based on Tree Matching. J. Comput.-Aided Mol Des. 1998, 12, 471-490.
18. Venkatasubramanian, V.; Chan, K.; Caruthers, J. M. Evolutionary Design of Molecules with Desired Properties using the Genetic Algorithm. J. Chem. Inf. Comput. Sci. 1995, 55, 188-195.
19. 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.
20. Kamphausen, S.; Höltge, N.; Wirsching, F.; Morys-Wortmann, C.; Riester, D.; Goetz, R.; Thürk, M.; Schwienhorst, A. Genetic Algorithm for the Design of Molecules with Desired Properties. J. Comput.-Aided Mol. Des. 2002, 16, 551-567.
21. Nachbar, R. B. Molecular Evolution: Automated Manipulation of Hierarchical Chemical Topology and Its Application to Average Molecular Structures. Genetic Programming Evoluable Machines 2000, 1, 57-94.
22. Weininger, D. Method and Apparatus for Designing Molecules with Desired Properties by Evolving Successive Populations. U.S. Patent No. 5,434,796, 1995.
23. Globus, A.; Lawton, J.; Wipke, W. T. Automatic Molecular Design Using Evolutionary Algorithms. Nanotechnology 1999, 10, 290-299.
24. The Tripos Mol2 File Format is available from Tripos Inc. at http:// www.tripos.com/.
25. Diestel, R. Graph Theory, 2nd ed.; Springer-Verlag: New York, 2000.
26. Cross, A. D. J.; Wilson, R. C.; Hancock, E. R. Inexact Graph Matching using Genetic Search. Pattern Recognit. 1997, 30, 953-970.
27. Brown, N. Generation and Display of Activity-Weighted Chemical Hyperstructures, Ph.D. Thesis, The University of Sheffield, UK, 2002.
28. Jiang, X.; Münger, A.; Bunke, H. On Median Graphs: Properties, Algorithms, and Applications. IEEE Trans. Patt. Anal. Mach. Intell. 2001, 23, 1144-1151.
29. Shapiro, L. G.; Haralick, R. M. Structural Descriptions and Inexact Matching. IEEE Trans. Patt. Anal. Mach. Intell. 1981, 3, 504-519.
30. Fonseca, C. M.; Fleming, P. J. Genetic Algorithms for Multiobjective Optimisation: Formulation, Discussion and Generalization. In Genetic Algorithms: Proceedings of the Fifth International Conference; Forrest, S., Ed.; Morgan Kaufmann: San Mateo, CA, 1993; pp 416-423.
31. Handschuh, S.; Wagener, M.; Gasteiger, J. Superposition of Three-Dimensional Chemical Structures Allowing for Conformational Flexibility by a Hybrid Method. J. Chem. Inf. Comput. Sci. 1998, 38, 220-232.
32. Agrafiotis, D. K. Multiobjective Optimisation of Combinatorial Libraries. IBM J. Res. Dev. 2001, 45, 545-566.
33. Wright, T.; Gillet, V. J.; Green, D. V. S.; Pickett, S. D. Optimizing the Size and Configuration of Combinatorial Libraries. J. Chem. Inf. Comput. Sci. 2003, 43, 381-390.
34. The NCI AIDS database available from http://dtp.nci.nih.gov.
35. The Grid: Blueprint for a New Computing Infrastructure; Foster, I., Kesselman, C., Eds.; Morgan Kaufmann: San Francisco, CA, 1999.
36. Horn, J.; Nafpliotis, N.; Goldberg, D. E. A Niched Pareto Genetic Algorithm for Multiobjective Optimisation. In Proceedings of the First IEEE Conference on Evolutionary Computation; IEEE: New York, 1994; pp 82-87.
37. Brown, N.; Lewis, R. A.; Willett, P.; Wilton, D. J. Generation and Display of Activity-Weighted Chemical Hyperstructures. J. Chem. Inf. Comput. Sci. 2003, 43, 288-297.
38. de Julián-Ortiz, J. V. Virtual Darwinian Drug Design: QSAR Inverse Problem, Virtual Combinatorial Chemistry, and Computational Screening. Comb. Chem. High Throughput Screening 2001, 4, 295-310.