References
Good, A.C. and Mason, J.S., Three-dimensional structure database searches, Rev. Comput. Chem., 7 (1995) 67–117.
Barnard, J.M., Substructure searching methods: Old and new, J. Chem. Inf. Comput. Sci., 33 (1993) 532–538.
Downs, G.M. and Willett, P., Similarity searching in databases of chemical structures, Rev. Comput. Chem., 7 (1995) 1–66.
Sadowski, J. and Gasteiger, J., From atoms and bonds to three-dimensional atomic coordinates: Automatic model builders, Chem. Rev., 93 (1993) 2567–2581.
Martin, Y.C. and Willett, P. (Eds.), Designing bioactive molecules: Three-dimensional techniques and applications (in press).
Pepperrell, C.A., Willett, P. and Taylor, R., Implementation and use of an atom-mapping procedure for similarity searching in databases of 3D chemical structures, Tetrahedron Comput. Methodol., 3 (1990) 575–593.
Perry, N.C. and van Geerestein, V.J., Database searching on the basis of three-dimensional molecular similarity using the SPERM program, J. Chem. Inf. Comput. Sci., 32 (1992) 607–616.
Fisanick, W., Cross, K.P. and Rusinko, A., Similarity searching of CAS Registry substances: 1. Global molecular property and generic atom triangle geometric searching, J. Chem. Inf. Comput. Sci., 32 (1992) 664–674.
Bemis, G.W. and Kuntz, I.D., A fast and efficient method for 2D and 3D molecular shape description, J. Comput.-Aided Mol. Design, 6 (1992) 607–628.
Nilakantan, R., Bauman, N. and Venkataraghavan, R., A new method for rapid characterisation of molecular shape: Applications in drug design, J. Chem. Inf. Comput. Sci., 33 (1993) 79–85.
Bath, P.A., Poirrette, A.R., Willett, P. and 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., 34 (1994) 141–147.
Good, A.C., Ewing, T.J.A., Gschwend, D.A. and Kuntz, I.D., New molecular shape descriptors: Application in database screening, J. Comput.-Aided Mol. Design, 9 (1995) 1–12.
Burt, C., Richards, W.G. and Huxley, P., The application of molecular similarity calculations, J. Comput. Chem., 11 (1990) 1139–1146.
Manaut, F., Sanz, F., Jose, J. and Milesi, M., Automatic search for maximum similarity between molecular electrostatic potential distributions, J. Comput.-Aided Mol. Design, 5 (1991) 371–380.
Richard, A.M., Quantitative comparison of molecular electrostatic potentials for structure-activity studies, J. Comput. Chem., 12 (1991) 959–969.
Good, A.C., Hodgkin, E.E. and Richards, W.G., The utilisation of Gaussian functions for the rapid evaluation of molecular similarity, J. Chem. Inf. Comput. Sci., 32 (1992) 188–191.
Sanz, F., Manaut, F., Rodriguez, J., Lozoya, E. and Lopez-de-Brinas, E., MEPSIM: A computational package for analysis and comparison of molecular electrostatic potentials, J. Comput.-Aided Mol. Design, 7 (1993) 337–347.
Petke, J.D., Cumulative and discrete similarity analysis of electrostatic potentials and fields, J. Comput. Chem., 14 (1993) 928–933.
Good, A.C., Peterson, S.J. and Richards, W.G., QSARS from similarity matrices: Technique validation and application in the comparison of different similarity evaluation methods, J. Med. Chem., 36 (1993) 2929–2937.
Burt, C., Molecular similarity calculations for the rational design of bioactive molecules, In Vinter, J.G. and Gardner, M. (Eds.) Molecular modelling and drug design, Macmillan, London, 1994, pp. 305–332.
Johnson, M.A., Maggiora, G.M., Lajiness, M.S., Moon, J.B., Petke, J.D. and Rohrer, D.C., Rational use of chemical and sequence databases, In van de Waterbeemd, H. (Ed.) Advanced computer-assisted techniques in drug discovery, VCH, Weinheim, 1995, pp. 89–110.
Wild, D.J. and 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., 36 (1996) 159–167.
Thorner, D.A., Wild, D.J., Willett, P. and 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., 36 (1996) 900–908.
Thorner, D.A., Willett, P., Wright, P.M. and Taylor, R., Similarity searching in files of three-dimensional chemical structures: Representation and searching of molecular electrostatic potentials using field-graphs, J. Comput.-Aid. Mol. Design, 11 (1997) 163–174.
Bures, M.G., Martin, Y.C. and Willett, P., Searching techniques for databases of three-dimensional chemical structures, Topics Stereochem., 21 (1994) 467–511.
Ho, C.M.W. and Marshall, G.R., FOUNDATION: A program to retrieve all possible structures containing a user-defined number of matching query elements from three-dimensional databases, J. Comput.-Aid. Mol. Design, 7 (1993) 3–22.
Moon, J.B. and Howe, W.J., 3D database searching and de novo construction models in molecular design, Tetrahedron Comput. Methodol., 3 (1990) 697–711.
Carbo, R., Leyda, L. and Arnau, M., How similar is a molecular to another? An electron density measure of similarity between two molecular structures, Int. J. Quant. Chem., 17 (1980) 1185–1189.
Bron, C. and Kerbosch, J., Algorithm 457: Finding all cliques of an undirected graph, Comm. ACM, 16 (1973) 575–577.
Brint, A.T. and Willett, P., Algorithms for the identification of three-dimensional maximal common substructures, J. Chem. Inf. Comput. Sci., 27 (1987) 152–158.
CONCORD is distributed by the University of Texas at Austin and Tripos Inc., St Louis, MO, U.S.A.
Stewart, J.J.M., MOPAC: a semiempirical molecular orbital program, J. Comput.-Aided Mol. Design, 4 (1990) 1–105.
Goldberg, D.E., Genetic Algorithms in Search, Optimisation and Machine Learning, Addison-Wesley, New York, 1989.
Michaelewicz, Z., Genetic Algorithms + Data Structures = Evolution Programs, 2nd Ed., Springer Verlag, New York, 1994.
Willett, P., Genetic algorithms in molecular recognition and design, Trends Biotech., 13 (1995) 516–521.
Clark, D.E. and Westhead, D.R., Evolutionary algorithms in computer-aided molecular design, J. Comput.-Aided Mol. Design, 10 (1996) 337–358.
Payne, A.W.R. and Glen, R.C., Molecular recognition using a binary genetic search algorithm, J. Mol. Graph., 11 (1993) 74–91.
Willett, P., Similarity searching and clustering algorithms for processing database of two-dimensional and three-dimensional chemical structures, In Dean, P.M. (Ed.), Molecular similarity in drug design, Chapman and Hall, Glasgow, 1994, pp. 110–137.
Johnson, M.A. and Maggiora, G.M. (Eds.), Concepts and Applications of Molecular Similarity, John Wiley, New York, 1990.
Siegal, S., Nonparametric Statistics for the Behavioural Sciences, McGraw-Hill Kogakusha, Tokyo, 1956.
Reynolds, C.A., Essex, J.W. and Richards, W.G., Atomic charges for variable molecular conformations, J. Am. Chem. Soc., 114 (1992) 9075–9079.
Clark, D.E., Willett, P. and Kenny, P.W., Pharmacophoric pattern matching in files of three-dimensional chemical structures: Use of smoothed-bounded distance matrices for the representation and searching of conformationally-flexible molecules, J. Mol. Graph., 10 (1992) 194–204.
Moock, T.E., Henry, D.R., Ozkabak, A.G. and Alamgir, M., Conformational searching in ISIS/3D databases, J. Chem. Inf. Comput. Sci., 34 (1991) 184–189.
Hurst, T., Flexible 3D searching: The directed tweak technique, J. Chem. Inf. Comput. Sci., 34 (1994) 190–196.
Milne, G.W.A., Nicklaus, M.C., Driscoll, J.S. and Wang, S., National Cancer Institute Drug Information System 3D Database, J. Chem. Inf. Comput. Sci., 34 (1994) 1219–1224.
Smellie, A., Kahn, S.D. and Teig, S.L., Analysis of conformational coverage: 1. Validation and estimation of coverage, J. Chem. Inf. Comput. Sci., 35 (1995) 285–294.
Smellie, A., Kahn, S.D. and Teig, S.L., Analysis of conformational coverage: 2. Applications of con-formational models, J. Chem. Inf. Comput. Sci., 35 (1995) 295–304.
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. and Watson, D.G., The development of Versions 3 and 4 of the Cambridge Structural Database System, J. Chem. Inf. Comput. Sci., 31 (1991) 187–204.
Ghose, A.K., Jaeger, E.P., Kowalczyk, P.J., Peterson, M.L. and Treasurywala, A.M., Conformational searching methods for small molecules: 1. Study of the SYBYL search method, J. Comput. Chem., 14 (1993) 1050–1065.
Pepperrell, C.A. and Willett, P., Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances, J. Comput.-Aid. Mol. Design, 5 (1991) 455–474.
Henry, D.R., Jurs, P.C. and Denny, W.A., Structure-antitumour activity relationships of 9-anilino-acridines, J. Med. Chem., 25 (1982) 899–908.
Stuper, A.J. and Jurs, P.C., Structure-activity studies of barbiturates using pattern-recognition techniques, J. Pharm. Sci., 67 (1978) 745–751.
Chastrette, M., Zakarya, D. and Elmouaffek, A., Structure-odor relations of the nitrobenzene musk family, Eur. J. Med. Chem., 21 (1996) 505–510.
Yuta, K. and Jurs, P.C., Computer-assisted structure-activity studies of chemical carcinogens: Aromatic amines, J. Med. Chem., 24 (1981) 241–251.
Stouch, T.R. and Jurs, P.C., Computer-aided studies of the structure-activity relationships between some steroids and their anti-inflammatory activity, J. Med. Chem., 29 (1986) 2125–2136.
Rose, S.L. and Jurs, P.C., Computer-assisted studies of structure-activity relationships of N-nitroso compounds using pattern recognition, J. Med. Chem., 25 (1982) 769–776.
Kearsley, S.K., Sallamack, S., Fluder, E.M., Andose, J.D., Mosley, R.T. and Sheridan, R.P., Chemical similarity using physicochemical property descriptors, J. Chem. Inf. Comput. Sci., 36 (1996) 118–127.
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Thorner, D.A., Wild, D.J., Willett, P. et al. Calculation of structural similarity by the alignment of molecular electrostatic potentials. Perspectives in Drug Discovery and Design 9, 301–320 (1998). https://doi.org/10.1023/A:1027228509338
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DOI: https://doi.org/10.1023/A:1027228509338