Journal of Computer-Aided Molecular Design

, Volume 5, Issue 5, pp 455–474 | Cite as

Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances

  • Catherine A. Pepperrell
  • Peter Willett
Research Papers


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.

Key words

Inter-atomic distances Similarity searching Structure matching algorithms Three-dimensional chemical structure databases 


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  1. 1.
    Barnard, J.M., Perspect. Inform. Manage 1 (1989) 133.Google Scholar
  2. 2.
    Lipscombe, K.J., Lynch, M.F. and Willett, P.. Annu. Rev. Inform. Sci. Technol., 24 (1989) 189.Google Scholar
  3. 3.
    Willett, P., Similarity and Clustering in Chemical Information Systems, Research Studies Press, Letchworth, Herts., U.K., 1987.Google Scholar
  4. 4.
    Johnson, M.A., J. Math. Chem., 3 (1989) 117.Google Scholar
  5. 5.
    Adamson, G.W. and Bush, J.A., Inform. Stor. Retr., 9 (1973) 561.Google Scholar
  6. 6.
    Carhart, R.E., Smith, D.H. and Venkataraghavan, R., J. Chem. Inform. Comput. Sci., 25 (1985) 64.Google Scholar
  7. 7.
    Johnson, M.A. and Maggiora, G.M., Concepts and Applications of Molecular Similarity, John Wiley, New York, 1990.Google Scholar
  8. 8.
    Willett, P., Winterman, V. and Bawden, D., J. Chem. Inform. Comput. Sci., 26 (1986) 36.Google Scholar
  9. 9.
    Johson, M.A., Lajiness, M. and Maggiora, G.M., Prog. Clin. Biol. Res., 291 (1989) 167.Google Scholar
  10. 10.
    Lajiness, M.S., Johnson, M.A. and Maggiora, G.M., Prog. Clin. Biol. Res., 291 (1989) 173.Google Scholar
  11. 11.
    Willett, P. and Winterman, V., Quant. Struct.-Act. Relat., 5 (1986) 18.Google Scholar
  12. 12.
    VanDrie, J.H., Weininger, D. and Martin, Y.C., J. Comput.-Aided Mol. Design, 3 (1989) 225.Google Scholar
  13. 13.
    Sheridan, R.P., Nilakantan, R., Rusinko, A., Bauman, N., Haraki, K.S. and Venkataraghavan, R., J. Chem. Inform. Comput. Sci., 29 (1989) 255.Google Scholar
  14. 14.
    Jakes, S.E., Watts, N.J., Bawden, D. and Fisher, J.D., J. Mol. Graphics, 5 (1987) 41.Google Scholar
  15. 15.
    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.Google Scholar
  16. 16.
    Murrall, N.W. and Davies, E.K., J. Chem. Inform. Comput. Sci., 30 (1990) 312.Google Scholar
  17. 17.
    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.Google Scholar
  18. 18.
    Jakes, S.E. and Willett, P., J. Mol. Graphics, 4 (1986) 12.Google Scholar
  19. 19.
    Pepperrell, C.A., Poirrette, A.R., Willett, P. and Taylor, R., Pesticide Sci., in press.Google Scholar
  20. 20.
    Klopman, G. and Raychaudhury, C., J. Chem. Inform. Comput. Sci., 30 (1990) 12.Google Scholar
  21. 21.
    Mitchell, E.M., Allen, F.H., Mitchell, G.F. and Rowland, R.S., Proc. 2nd International Conference on Chemical Structures, in press.Google Scholar
  22. 22.
    Vladutz, G.E., In Willett, P. (ed.) Modern Approaches to Chemical Reaction Searching, Gower, Aldershot, 1986, pp. 202–220.Google Scholar
  23. 23.
    Brint, A.T. and Willett, P., J. Chem. Inform. Comput. Sci., 27 (1987) 152.Google Scholar
  24. 24.
    Ormerod, A., Willett, P. and Bawden, D., Quant. Struct.-Act. Relat., 8 (1989) 115.Google Scholar
  25. 25.
    Jurs, P.C., Stouch, T.R., Czerwinski, M. and Narvaez, J.N., J. Chem. Inform. Comput. Sci., 25 (1985) 296.Google Scholar
  26. 26.
    Jurs, P.C., Chou, J.T., and Yuan, M., J. Med. Chem., 22 (1979) 476.Google Scholar
  27. 27.
    Rose, S.L. and Jurs, P.C., J. Med. Chem., 25 (1982) 769.Google Scholar
  28. 28.
    Yuta, K. and Jurs, P.C., J. Med. Chem., 24 (1981) 241.Google Scholar
  29. 29.
    Chastrette, M., Zakarya, D. and Elmouaffek, A., Eur. J. Med. Chem., 21 (1986) 505.Google Scholar
  30. 30.
    DeFlora, S., Koch, R., Strobel, K. and Nagel, M., Toxicol. Environ. Chem., 10 (1980) 157.Google Scholar
  31. 31.
    Walsh, D.B. and Claxton, L.D., Mutat. Res., 182 (1987) 55.Google Scholar
  32. 32.
    Henry, D.R., Jurs, P.C. and Denny, W.A., J. Med. Chem., 25 (1982) 899.Google Scholar
  33. 33.
    Stouch, T.R. and Jurs, P.C., J. Med. Chem., 29 (1986) 2125.Google Scholar
  34. 34.
    Stuper, A.J. and Jurs, P.C., J. Pharm. Sci., 67 (1978) 745.Google Scholar
  35. 35.
    Rusinko, A., Sheridan, R.P., Nilakantan, R., Haraki, K.S., Bauman, N. and Venkataraghavan, R., J. Chem. Inform. Comput. Sci., 29 (1989) 252.Google Scholar
  36. 36.
    Dolata, P.D., Leach, A.R. and Prout, K., J. Comput.-Aided Mol. Design, 1 (1987) 73.Google Scholar
  37. 37.
    Pepperrell, C.A., Ph.D. thesis, University of Sheffield, in preparation.Google Scholar
  38. 38.
    Siegel, S. and Castellan, N.J., Nonparametric Statistics, 2nd edn., McGraw-Hill, New York, 1988, p. 399.Google Scholar
  39. 39.
    Levi, G., Calcolo, 9 (1972) 341.Google Scholar
  40. 40.
    Brint, A.T. and Willett, P., J. Comput.-Aided Mol. Design, 2 (1988) 311.Google Scholar
  41. 41.
    Danziger, D.J. and Dean, P.M., J. Theoret. Biol., 116 (1985) 215.Google Scholar
  42. 42.
    McGregor, J.J., Software-Pract. Exp., 12 (1982) 23.Google Scholar
  43. 43.
    Kier, L.B., Med. Res. Rev., 7 (1987) 417.Google Scholar

Copyright information

© ESCOM Science Publishers B.V 1991

Authors and Affiliations

  • Catherine A. Pepperrell
    • 1
  • Peter Willett
    • 1
  1. 1.Department of Information StudiesUniversity of SheffieldSheffieldU.K.

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