Similarity searching in files of three-dimensional chemical structures: Flexible field-based searching of molecular electrostatic potentials

Journal of Chemical Information and Computer Sciences

Volumn 36, Issue 4, 1996, Pages 900-908

  Thorner, David A ^a   Wild, David J ^a   Willett, Peter ^a   Wright, P Matthew ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000132991     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci960002w     Document Type: Article

References (42)

1. Sadowski, J.; Gasteiger, J. From Atoms and Bonds to Three-Dimensional Atomic Co-ordinates: Automatic Model Builders. Chem. Rev. 1993, 93, 2567-2581.
2. Ricketts, E. M.; Bradshaw, J.; Hann, M.; Hayes, F.; Tanna, N.; Ricketts, D. M. Comparison of Conformations of Small Molecules from the Protein Data Bank with Those Generated by Concord, Cobra, ChemDBS-3D and Converter, and Those Extracted from the Cambridge Structural Database. J. Chem. Inf. Comput. Sci. 1993, 33, 905-925.
3. Bures, M. G.; Martin, Y. C.; Willett, P. Searching Techniques for Databases of Three-Dimensional Chemical Structures. Topics Stereo-chem. 1994, 21, 467-511.
4. Jakes, S. E.; Watts, N. J.; Willett, P.; Bawden, D.; Fisher, J. D. Pharmacophoric Pattern Matching in Files of Three-Dimensional Chemical Structures: Evaluation of Search Performance. J. Mol. Graphics 1987, 5, 41-48.
5. Sheridan, R. P.; Nilakantan, R.; Rusinko, A.; Bauman, N.; Haraki, K. S.; Venkataraghavan, R. 3DSEARCH: a System for Three-Dimensional Substructure Searching. J. Chem. Inf. Comput. Sci. 1989, 29, 255-260.
6. Murrall, N. W.; Davies, E. K. Conformational Freedom in 3-D databases. 1. Techniques. J. Chem. Inf. Comput. Sci. 1990, 30, 312-316.
7. Clark, D. E.; Willett, P.; Kenny, P. W. Pharmacophoric Pattern Matching in Files of Three-Dimensional Chemical Structures: Use of Smoothed-Bounded Distances Matrices for the Representation and Searching of Conformationally-Flexible Molecules. J. Mol. Graphics 1992, 10, 194-204.
8. 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.
9. Hurst, T. Flexible 3D Searching: the Directed Tweak Technique. J. Chem. Inf. Comput. Sci. 1994, 34, 190-196.
10. Moock, T. E.; Henry, A. G.; Ozkabak, A. G.; Alamgir, M. Conformational Searching in ISIS/3D Databases. J. Chem. Inf. Comput. Sci. 1994, 34, 184-189.
11. Greene, J.; Kahn, S.; Savoj, H.; Sprague, P.; Teig, S. Chemical Function Queries for 3D Database Search. J. Chem. Inf. Comput. Sci. 1994, 34, 1297-1308.
12. Milne, G. W. A.; Nicklaus, M. C.; Driscoll, J. S.; Wang, S. National Cancer Institute Drug Information System 3D Database. J. Chem. Inf. Comput. Sci. 1994, 34, 1219-1224.
13. Molecular Similarity in Drug Design; Dean, P. M., Ed.; Chapman and Hall: Glasgow, 1995.
14. Downs, G. M.; Willett, P. Similarity Searching in Databases of Chemical Structures. Rev. Comput. Chem. 1995, 7, 1-66.
15. 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. Methodol. 1990, 3, 575-593.
16. Fisanick, W.; Cross, K. P.; Rusinko, A. Similarity Searching of CAS Registry Substances. 1. Global Molecular Property and Generic Atom Triangle Geometric Searching. J. Chem. Inf. Comput. Sci. 1992, 32, 664-674.
17. 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.
18. Ho, C. M. W.; Marshall, G. R. FOUNDATION: a Program to Retrieve All Possible Structures Containing a User-Defined Minimum Number of Matching Query Elements from Three-Dimensional Databases. J. Computer-Aided Mol. Design 1993, 7, 3-22.
19. 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.
20. Good, A. C.; Ewing, T. J. A.; Gschwend, D. A.; Kuntz, I. D. New Molecular Shape Descriptors: Application in Database Screening. J. Computer-Aided Mol. Design 1995, 9, 1-12.
21. Turner, D. B.; Willett, P.; Ferguson, A. M.; 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.
22. Wild, D. J.; Willett, P. Similarity Searching in Files of Three-Dimensional Chemical Structures: Alignment of Molecular Electrostatic Potentials with a Genetic Algorithm. J. Chem. Inf. Comput. Sci. 1996, in press.
23. Thorner, D. A.; Willett, P.; Wright, P. M.; Taylor, R. Similarity Searching in Files of Three-Dimensional Chemical Structures: Representation and Searching of Molecular Electrostatic Potentials Using Field-Graphs. Manuscript in preparation.
24. Burt, C.; Richards, W. H.; Huxley, P. The Application of Molecular Similarity Calculations. J. Comput. Chem. 1990, 11, 1139-1146.
25. Good, A. C.; Hodgkin, E. E.; Richards, W. G. The Utilisation of Gaussian Functions for the Rapid Evaluation of Molecular Similarity. J. Chem. Inf. Comput. Sci. 1992, 32, 188-191.
26. Good, A. C.; Peterson, S. J.; Richards, W. G. QSARS from Similarity Matrices. Technique Validation and Application in the Comparison of Different Similarity Evaluation Methods. J. Med. Chem. 1993, 36, 2929-2937.
27. Wright, P. M. Ph.D. Thesis, University of Sheffield, Manuscript in preparation.
28. Kuhl, F. S.; Crippen, G. M.; Friesen, D. K. A Combinatorial Algorithm for Calculating Ligand Binding. J. Comput. Chem. 1984, 5, 24-34.
29. Brint, A. T.; Willett, P. Algorithms for the Identification of Three-Dimensional Maximal Common Substructures. J. Chem. Inf. Comput. Sci. 1987, 27, 152-158.
30. Goldberg, D. E. Genetic Algorithms in Search, Optimization and Machine Learning; Addison Wesley: New York, 1989.
31. Forrest, S. Genetic Algorithms: Principles of Natural Selection Applied to Computation. Science 1993, 261, 872-878.
32. Goldberg, D. E. Genetic and Evolutionary Algorithms Come of Age. Commun. ACM 1994, 37(3), 113-119.
33. Willett, P. Genetic Algorithms in Molecular Recognition and Design. Trends Biotechnol. 1995, 143, 516-521.
34. CONCORD is distributed by Tripos Associates, St. Louis. MO 63144, U.S.A.
35. Reynolds, C. A.; Essex, J. W.; Richards, W. G. Atomic Charges for Variable Molecular Conformations. J. Am. Chem. Soc. 1992, 114, 9075-9079.
36. Stewart, J. J. M. MOPAC: a Semi-Empirical Molecular Orbital Program. J. Computer-Aided Mol. Design 1990, 4, 1-105.
37. Smellie, A.; Kahn, S. D.; Teig, S. L. Analysis of Conformational Coverage. 1. Validation and Estimation of Coverage. J. Chem. Inf. Comput. Sci. 1995, 35, 285-294.
38. Smellie, A.; Kahn, S. D.; Teig, S. L. Analysis of Conformational Coverage. 2. Applications of Conformational Models. J. Chem. Inf. Comput. Sci. 1995, 35, 295-304.
39. Chose, A. K.; Jaeger, E. P.; Kowalczyk, P. J.; Peterson, M. L.; Treasurywala, A. M. Conformational searching methods for small molecules. 1. Study of the SYBYL search method. J. Comput. Chem 1993, 14, 1050-1065.
40. Allen, F. H.; Davies, J. E.; Galloy, J. J.; Johnson, O.; Kennard, O.; Macrae, C. F.; Mitchell, E. M.; Mitchell, G. F.; Smith, J. M.; Watson, D. G. The Development of Versions 3 and 4 of the Cambridge Structural Database System. J. Chem. Inf. Comput. Sci. 1991, 31, 187-204.
41. Allen, F. H.; Kennard, O. 3D Search and Research Using the Cambridge Structural Database. Chem. Design Automation News 1993, 8(1), 31-37.
42. Leach, A. R. An Algorithm to Directly Identify a Molecule's "Most Different" Conformations. J. Chem. Inf. Comput. Sci. 1994, 34, 661-670.