Summary
We have developed a program, HookSpace, which provides a simplistic approach to assessing the diversity of molecular databases. The spatial relationship between pairs of intramolecular functional groups can be analysed in a variety of ways to provide both qualitative and quantitative measures of diversity. Results are described and contrasted for two commercially available databases and a combinatorial library of benzodiazepam derivatives. HookSpace highlights the main differences in molecular content of these data sets.
Similar content being viewed by others
References
Verlinde, C.L.M.J. and Hol, W.G.J., Structure, 2 (1994) 577.
Kuntz, I.D., Meng, E.C. and Shoichet, B.K., Acc. Chem. Res., 27 (1994) 117.
Moon, J.B. and Howe, W.J., Protein Struct. Funct. Genet., 11 (1991) 314.
Jones, G., Willett, P. and Glen, R.C., J. Mol. Biol., 245 (1995) 43.
DesJarlais, R.L., Sheridan, R.P., Seibel, G.L., Dixon, J.S., Kuntz, I.D. and Venkataraghavan, R., J. Med. Chem., 28 (1988) 849.
Lawrence, M.C. and Davis, P.C., Protein Struct. Funct. Genet., 12 (1992) 31.
Eisen, M.B., Wiley, D.C., Karplus, M. and Hubbard, R.E., Protein Struct. Funct. Genet., 19 (1994) 199.
Alper, J., Science, 264 (1994) 1399.
Keanan, J.K., Tsai, D.E. and Keene, J.D., Trends Biochem. Sci., 19 (1994) 57.
Dunbar, Jr., J.B., Abs. Papers Am. Chem. Soc., 208 (1994) 124.
Martin, E.J., Blaney, J.M., Siani, M.A., Spellmeyer, D.C., Wong, A.K. and Moos, W.H., J. Med. Chem., 38 (1995) 1431.
Lauri, G. and Bartlett, P.A., J. Comput.-Aided Mol. Design, 8 (1994) 51.
Allen, F.H., Bellard, S., Brice, M.D., Cartwright, B.A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B.G., Kennard, O., Motherwell, W.D.W., Rodgers, J.R. and Watson, D.G., Acta Crystallogr., B 35 (1979) 2331.
ACD-3D, v. 93.1, available from Molecular Design Ltd, San Leandro, CA.
CONCORD, available from Tripos Associates Inc., St. Louis, MO.
Allinger, N.L., J. Am. Chem. Soc., 99 (1977) 8127.
Bunin, B.A. and Ellman, J.A., J. Am. Chem. Soc., 114 (1992) 10997.
Oldfield, T.J., J. Mol. Graphics, 10 (1992) 247.
Nakai, H., Acta Crystallogr., C 45 (1989) 1465.
Larson, K. and Von, Sydow, E., Acta Crystallogr. Scand., 20 (1966) 1465.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Boyd, S.M., Beverley, M., Norskov, L. et al. Characterising the geometric diversity of functional groups in chemical databases. J Computer-Aided Mol Des 9, 417–424 (1995). https://doi.org/10.1007/BF00123999
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00123999