Similarity searching in files of three-dimensional chemical structures. Alignment of molecular electrostatic potential fields with a genetic algorithm

Journal of Chemical Information and Computer Sciences

Volumn 36, Issue 2, 1996, Pages 159-167

  Wild, David J ^a   Willett, Peter ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000132994     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci9500851     Document Type: Article

References (56)

1. Downs, G. M.; Willett, P. Similarity Searching in Databases of Chemical Structures. Rev. Comput. Chem. 1995, 7, 1-66.
2. Willett, P. Similarity and Clustering in Chemical Information Systems; Research Studies Press: Letchworth, 1987.
3. Barnard, J. M.; Downs, G. M. Clustering of Chemical Structures on the Basis of Two-Dimensional Similarity Measures. J. Chem. Inf. Comput. Sci. 1992, 32, 644-649.
4. Chemical Structure Systems; Ash, J. E., Warr, W. A., Willett, P., Eds.; Ellis Horwood: Chichester, 1991.
5. Pepperrell, C. A.; Willett, P.; Taylor, R. Implementation and Use of an Atom-Mapping Procedure for Similarity Searching in Databases of 3-D Chemical Structures. Tetrahedron Comput. Methodology 1990, 3, 575-593.
6. Bemis, G. W.; Kuntz, I. D. A Fast and Efficient Method for 2D and 3D Molecular Shape Description. J. Comput.-Aided Mol. Design 1992, 6, 607-628.
7. Perry, N. C.; van Geerestein, V. J. Database Searching on the Basis of Three-Dimensional Molecular Similarity Using the SPERM Program. J. Chem. Inf. Comput. Sci. 1992, 32, 607-616.
8. Nilakantan, R.; Bauman, N.; Venkataraghavan, R. A New Method for Rapid Characterisation of Molecular Shape: Applications in Drug Design. J. Chem. Inf. Comput. Sci. 1993, 33, 79-85.
9. Bath, P. A.; Poirrette, A. R.; Willett, P.; Allen, F. H. Similarity Searching in Files of Three-Dimensional Chemical Structures: Comparison of Fragment-Based Measures of Shape Similarity. J. Chem. Inf. Comput. Sci. 1994, 34, 141-147.
10. van Geerestein, V. J.; Perry, N. C.; Grootenhuis, P. G.; Haasnoot, C. A. G. 3D Database Searching on the Basis of Ligand Shape Using the SPERM Prototype Method. Tetrahedron Comput. Methodology 1990, 3, 595-613.
11. Downs, G. M.; Willett, P.; Fisanick, W. Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data. J. Chem. Inf. Comput. Sci. 1994, 34, 1094-1102.
12. 3D QSAR in Drug Design; Kubinyi, H., Ed.; ESCOM: Leiden, 1993.
13. Molecular Modelling and Drug Design; Vinter, J. G., Gardner, M., Eds.; Macmillan: London, 1994.
14. Thorner, D. A. Electrostatic Field Searching in Databases of Three-Dimensional Chemical Structures; Ph.D. Thesis, University of Sheffield, 1995.
15. Turner, D. B.; Willett, P.; Ferguson, A.; Heritage, T. W. Similarity Searching in Files of Three-Dimensional Chemical Structures. Evaluation of Similarity Coefficients and Standardisation Methods for Field-Based Similarity Searching. SAR QSAR Environmental Res. 1995, 3, 101-130.
16. Manaut, F.; Sanz, F.; Jose, J.; Milesi, M. Automatic Search for Maximum Similarity Between Molecular Electrostatic Potential Distributions. J. Comput.-Aided Molecular Design 1991, 5, 371-380.
17. Burt, C.; Richards, W. H.; Huxley, P. The Application of Molecular Similarity Calculations. J. Comput. Chem. 1990, 11, 1139-1146.
18. Richard, A. M. Quantitative Comparison of Molecular Electrostatic Potentials for Structure-Activity Studies. J. Comput. Chem. 1991, 12, 959-969.
19. Petke, J. D. Cumulative and Discrete Similarity Analysis of Electrostatic Potentials and Fields. J. Comput. Chem. 1993, 14, 928-933.
20. Good, A. C.; Hodgkin, E. E.; Richards, W. G. The Utilization of Gaussian Functions for the Rapid Evaluation of Molecular Similarity. J. Chem. Inf. Comput. Sci. 1992, 32, 188-191.
21. Good, A. C.; Richards, W. G. Rapid Evaluation of Shape Similarity Using Gaussian Functions. J. Chem. Inf. Comput. Sci. 1993, 33, 112-116.
22. Goldberg, D. E. Genetic Algorithms in Search, Optimisation and Machine Learning; Addison-Wesley: New York, 1989.
23. Handbook of Genetic Algorithms; Davis, L., Ed.; Van Nostrand Reinhold: New York, 1991.
24. Forrest, S. Genetic Algorithms: Principles of Natural Selection Applied to Computation. Science 1993, 261, 872-878.
25. Goldberg, D. E. Genetic and Evolutionary Algorithms Come of Age. Commun. ACM 1994, 37(3), 113-119.
26. Blommers, M. J. J.; Lucasius, C. B.; Kateman, G.; Kaptein, R. Conformational Analysis of a Dinucleotide Photodimer with the Aid of the Genetic Algorithm. Biopolymers 1992, 32, 45-52.
27. Judson, R. S.; Jaeger, A. M.; Treasurywala, A. M.; Peterson, M. L. Conformational Searching Methods for Small Molecules: a Genetic Algorithm Approach. J. Comput. Chem. 1993, 14, 1407-1414.
28. Fontain, E. Application of Genetic Algorithms in the Field of Constitutional Similarity. J. Chem. Inf. Comput. Sci. 1992, 32, 748-752.
29. Payne, A. W. R.; Glen, R. C. Molecular Recognition Using a Binary Genetic Search Algorithm. J. Mol. Graphics 1993, 11, 74-91.
30. Brown, R. D.; Jones, G. J.; Willett, P.; Glen, R. C. Matching Two-Dimensional Chemical Graphs Using Genetic Algorithms. J. Chem. Inf. Comput. Sci. 1994, 34, 63-70.
31. Clark, D. E.; Jones, G.; Willett, P.; Kenny, P. W.; Glen, R. C. Pharmacophoric Pattern Matching in Files of Three-Dimensional Chemical Structures: Comparison of Conformational Searching Algorithms for Flexible Searching. J. Chem. Inf. Comput. Sci. 1994, 34, 197-206.
32. Jones, G.; Willett, P.; Glen, R. C. Molecular Recognition of Receptor Sites Using a Genetic Algorithm with a Description of Desolvation. J. Mol. Biol. 1995, 245, 43-53
33. Carbó, R.; Leyda, L.; Arnau, M. How Similar is a Molecule to Another? An Electron Density Measure of Similarity Between Two Molecular Structures. Int. J. Quantum Chem. 1980, 17, 1185-1189.
34. Sneath, P. H. A.; Sokal, R. R. Numerical Taxonomy; Freeman: San Francisco, CA, 1973.
35. Mühlenbein, H. How Genetic Algorithms Really Work. I. Mutation and Hill-Climbing; Proceedings of Parallel Problem Solving from Nature 2; Elsevier: Amsterdam, 1992.
36. Reeves, C. R. Using Genetic Algorithms with Small Populations. Proceedings of the Fifth International Conference on Genetic Algorithms; Forrest, S., Ed.; Morgan Kaufmann: San Mateo, CA, 1993; pp 92-99.
37. Wild, D. J. Structural and Electrostatic Similarity Searching in Three-Dimensional Chemical Databases Using Genetic Algorithms and Parallel Computers. Ph.D. Thesis, University of Sheffield, 1994.
38. Davis, L., Bit-Climbing, Representational Bias, and Test Suite Design, Proceedings of the Fourth International Conference on Genetic Algorithms, Morgan Kaufmann, San Mateo CA, 1991, 18-23.
39. Cramer, R. D.; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
40. CONCORD is distributed by the University of Texas at Austin and Tripos Associates, St. Louis, Missouri, U.S.A.
41. Stewart, J. J. M. MOPAC: a Semiempirical Molecular Orbital Program. J. Comput.-Aided Mol. Design 1990, 4, 1-105.
42. Siegal, S. Nonparametric Statistics for the Behavioral Sciences, McGraw-Hill: Kogakusha, Tokyo, 1956.
43. ASP. Automated Similarity Package User's Guide; Oxford Molecular Ltd.: Oxford, 1993.
44. KSR Parallel Programming; Kendal Square Research Corp.: Waltham, MA, 1992.
45. KSR C Programming; Kendal Square Research Corp.: Waltham, MA, 1992.
46. Tanase, R. Distributed Genetic Algorithms. Proceedings of the Third International Conference on Genetic Algorithms; Morgan Kaufmann: San Mateo, CA, 1989; pp 434-439.
47. Gordon, V. S.; Whitley, D. Serial and Parallel Genetic Algorithms as Function Optimizers. In Proceedings of the Fifth International Conference on Genetic Algorithms; Forrest, S., Ed..; Morgan Kaufmann: San Mateo, CA, 1993; pp 177-183.
48. Bianchini, R.; Brown, C. Parallel Genetic Algorithms on Distributed-Memory Architectures; University of Rochester Computer Science Department Technical Report 436; Rochester, NY, 1993.
49. Grefenstette, J. J. Parallel Adaptive Algorithms for Function Optimization. Technical Report CS-81-19; Vanderbilt University Computer Science Department: Nashville, TN, 1981.
50. Guha, S.; Majumdar, D.; Bhattacharjee, A. K. Molecular Electrostatic Potential: a Tool for the Prediction of the Pharmacophoric Pattern of Drug Molecules. J. Mol. Struct. (Theochem) 1992, 256, 61-74.
51. Pépe, G.; Siri, D.; Reboul, J. The Molecular Electrostatic Potential and Drug Design. J. Mol. Struct. (Theochem) 1992, 256, 175-185.
52. Burt, C. Molecular Similarity Calculations for the Rational Design of Bioactive Molecules. Molecular Modelling and Drug Design; Vinter, J. G., Gardner, M., Eds.; MacMillan: London, 1994; pp 305-332.
53. Reynolds, C. A.; Essex, J. W.; Richards, W. G. Atomic Charges for Variable Molecular Conformations. J. Am. Chem. Soc. 1992, 114, 9075-9079.
54. Moock, T. E.; Henry, D. R.; Ozkabak, A. G.; Alamgir, M. Conformational Searching in ISIS/3D Databases. J. Chem. Inf. Comput. Sci. 1994, 34, 184-189.
55. Hurst, T. Flexible 3D Searching: the Directed Tweak Technique. J. Chem. Inf. Comput. Sci. 1994, 34, 190-196.
56. Thorner, D. A.; Wild, D. J.; Willett, P.; Wright, P. M. Similarity Searching in Files of Three-Dimensional Chemical Structures. Flexible Field-Based Searching of Molecular Electrostatic Potentials. J. Chem. Inf. Comput. Sci. Submitted for publication.