Summary
This paper reports a comparison of several methods for measuring the degree of similarity between pairs of 3-D chemical structures that are represented by inter-atomic distance matrices. The methods that have been tested use the distance information in very different ways and have very different computational requirements. Experiments with 10 small datasets, for which both structural and biological activity data are available, suggest that the most cost-effective technique is based on a mapping procedure that tries to match pairs of atoms, one from each of the molecules that are being compared, that have neighbouring atoms at approximately the same distances.
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References
Barnard, J.M., Perspect. Inform. Manage 1 (1989) 133.
Lipscombe, K.J., Lynch, M.F. and Willett, P.. Annu. Rev. Inform. Sci. Technol., 24 (1989) 189.
Willett, P., Similarity and Clustering in Chemical Information Systems, Research Studies Press, Letchworth, Herts., U.K., 1987.
Johnson, M.A., J. Math. Chem., 3 (1989) 117.
Adamson, G.W. and Bush, J.A., Inform. Stor. Retr., 9 (1973) 561.
Carhart, R.E., Smith, D.H. and Venkataraghavan, R., J. Chem. Inform. Comput. Sci., 25 (1985) 64.
Johnson, M.A. and Maggiora, G.M., Concepts and Applications of Molecular Similarity, John Wiley, New York, 1990.
Willett, P., Winterman, V. and Bawden, D., J. Chem. Inform. Comput. Sci., 26 (1986) 36.
Johson, M.A., Lajiness, M. and Maggiora, G.M., Prog. Clin. Biol. Res., 291 (1989) 167.
Lajiness, M.S., Johnson, M.A. and Maggiora, G.M., Prog. Clin. Biol. Res., 291 (1989) 173.
Willett, P. and Winterman, V., Quant. Struct.-Act. Relat., 5 (1986) 18.
VanDrie, J.H., Weininger, D. and Martin, Y.C., J. Comput.-Aided Mol. Design, 3 (1989) 225.
Sheridan, R.P., Nilakantan, R., Rusinko, A., Bauman, N., Haraki, K.S. and Venkataraghavan, R., J. Chem. Inform. Comput. Sci., 29 (1989) 255.
Jakes, S.E., Watts, N.J., Bawden, D. and Fisher, J.D., J. Mol. Graphics, 5 (1987) 41.
Christie, B.D., Henry, D.R., Guner, O.F. and Moock, T.E., Online Information 90. Proceedings of the 14th International Online Information Meeting. Learned Information, Oxford, 1990, p. 137.
Murrall, N.W. and Davies, E.K., J. Chem. Inform. Comput. Sci., 30 (1990) 312.
Martin, Y.C., Bures, M.G. and Willett, P., In Lipkowitz, K.B. and Boyd, D.B. (Eds.) Reviews in Computational Chemistry, VCH, New York, 1990, pp. 213–263.
Jakes, S.E. and Willett, P., J. Mol. Graphics, 4 (1986) 12.
Pepperrell, C.A., Poirrette, A.R., Willett, P. and Taylor, R., Pesticide Sci., in press.
Klopman, G. and Raychaudhury, C., J. Chem. Inform. Comput. Sci., 30 (1990) 12.
Mitchell, E.M., Allen, F.H., Mitchell, G.F. and Rowland, R.S., Proc. 2nd International Conference on Chemical Structures, in press.
Vladutz, G.E., In Willett, P. (ed.) Modern Approaches to Chemical Reaction Searching, Gower, Aldershot, 1986, pp. 202–220.
Brint, A.T. and Willett, P., J. Chem. Inform. Comput. Sci., 27 (1987) 152.
Ormerod, A., Willett, P. and Bawden, D., Quant. Struct.-Act. Relat., 8 (1989) 115.
Jurs, P.C., Stouch, T.R., Czerwinski, M. and Narvaez, J.N., J. Chem. Inform. Comput. Sci., 25 (1985) 296.
Jurs, P.C., Chou, J.T., and Yuan, M., J. Med. Chem., 22 (1979) 476.
Rose, S.L. and Jurs, P.C., J. Med. Chem., 25 (1982) 769.
Yuta, K. and Jurs, P.C., J. Med. Chem., 24 (1981) 241.
Chastrette, M., Zakarya, D. and Elmouaffek, A., Eur. J. Med. Chem., 21 (1986) 505.
DeFlora, S., Koch, R., Strobel, K. and Nagel, M., Toxicol. Environ. Chem., 10 (1980) 157.
Walsh, D.B. and Claxton, L.D., Mutat. Res., 182 (1987) 55.
Henry, D.R., Jurs, P.C. and Denny, W.A., J. Med. Chem., 25 (1982) 899.
Stouch, T.R. and Jurs, P.C., J. Med. Chem., 29 (1986) 2125.
Stuper, A.J. and Jurs, P.C., J. Pharm. Sci., 67 (1978) 745.
Rusinko, A., Sheridan, R.P., Nilakantan, R., Haraki, K.S., Bauman, N. and Venkataraghavan, R., J. Chem. Inform. Comput. Sci., 29 (1989) 252.
Dolata, P.D., Leach, A.R. and Prout, K., J. Comput.-Aided Mol. Design, 1 (1987) 73.
Pepperrell, C.A., Ph.D. thesis, University of Sheffield, in preparation.
Siegel, S. and Castellan, N.J., Nonparametric Statistics, 2nd edn., McGraw-Hill, New York, 1988, p. 399.
Levi, G., Calcolo, 9 (1972) 341.
Brint, A.T. and Willett, P., J. Comput.-Aided Mol. Design, 2 (1988) 311.
Danziger, D.J. and Dean, P.M., J. Theoret. Biol., 116 (1985) 215.
McGregor, J.J., Software-Pract. Exp., 12 (1982) 23.
Kier, L.B., Med. Res. Rev., 7 (1987) 417.
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Pepperrell, C.A., Willett, P. Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances. J Computer-Aided Mol Des 5, 455–474 (1991). https://doi.org/10.1007/BF00125665
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DOI: https://doi.org/10.1007/BF00125665