Abstract
The objective of this work is to demonstrate that an appropriate treatment of quantum similarity matrices can reveal hidden data grouping related to relevant structural features and even to biological properties of interest. Classical scaling is used here to extract the information contained in the similarity relationships between the elements of a molecular set. Facet theory is invoked to relate, in a qualitative way, the spatial regions to structural characteristics as well as to properties of interest. Two application examples are discussed: the Cramer steriod set and a benzene, toluene and xylene derivatives set.
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References
Kubinyi, H. (Ed.) 3D QSAR in Drug Design: Theory,Methods and Applications, ESCOM, Leiden, The Netherlands, 1993.
Van de Waterbeemd, H., In Van de Waterbeemd, H. (Ed.) Structure-Property Correlations in Drug Research, Academic Press, San Diego, CA, 1996.
Dean, P.M. (Ed.) Molecular similarity in Drug Design, Blackie Academic & Professional, London, 1995.
Carbó, R., BesalÚ, E., Amat, L. and Fradera, X., J. Math. Chem., 18 (1995) 237.
Fradera, X., Amat, L., BesalÚ, E. and Carbó-Dorca, R., Quant. Struct.-Act. Relat., 16 (1997) 25.
Lobato, M., Amat, L., BesalÚ, E. and Carbó-Dorca, R., Quant. Struct.-Act. Relat., 16 (1997) 465.
Amat, L., Robert, D., BesalÚ, E. and Carbó-Dorca, R., J. Chem. Inf. Comput. Sci., 38 (1998) 624.
Robert, D. and Carbó-Dorca, R., J. Chem. Inf. Comput. Sci., 38 (1998) 620.
Amat, L., Carbó-Dorca, R. and Ponec, R., J. Comput. Chem., 19 (1998) 1575.
Robert, D. and Carbó-Dorca, R., Il Nuovo Cimento, A111 (1998) 1311.
Ponec, R., Amat, L. and Carbó-Dorca, R., Quantum Similarity approach to LFER: Substituent and solvent effects on the acidities of carboxylic acids, Technical Report: IT-IQC-98-14.
Mezey, P.G., Ponec, R., Amat, L. and Carbó-Dorca, R., Quantum Similarity approach to the characterization of molecular chirality, Technical Report: IT-IQC-98-16.
For a brief review of the QSAR studies on this data set, see, for example: Robert, D., Amat, L. and Carbó-Dorca, R., J. Chem. Inf. Comput. Sci., 39 (1999) 333.
Urrestarazu, E., Vaes, W.H.J., Verhaar, H.J.M. and Hermens, J.L.M. J. Chem. Inf. Comput. Sci., 38 (1998) 845.
Carbó, R., Arnau, J. and Leyda, L., Int. J. Quant. Chem., 17 (1980) 1185.
BesalÚ, E., Carbó, R., Mestres, J. and Solà, M., Top. Curr. Chem., 173 (1995) 31.
Carbó, R. and BesalÚ, E. In Carbó, R. (Ed.) Molecular Similarity and reactivity: from Quantum Chemical to Phenomenological approaches, Kluwer, Dordrecht, 1995.
R. Carbó-Dorca and P. G. Mezey (Eds.) Advances in Molecular Similarity, JAI Press, Greenwich, 1996.
Löwdin, P.O., Phys. Rev., 97 (1955) 1474, 1490.
McWeeny, R., Proc. R. Soc. London, A235 (1955) 496.
Carbó, R., BesalÚ, E., Amat, L. and Fradera, X., J. Math. Chem., 19 (1996) 47.
Robert, D. and Carbó-Dorca, R., J. Chem. Inf. Comput. Sci., 38 (1998) 469.
Cox, T.F. and Cox, M.A.A., Multidimensional Scaling, Chapman & Hall, London, 1994.
Eckart, C. and Young, G., Psychometrika, 1 (1936) 211.
Young, G. and Householder, A.S., Psychometrika, 3 (1938) 19.
Carroll, J.D. and Chang, J.J., IDIOSCAL (Individual Differences in Orientation SCAling): A generalization of INDSCAL allowing idiosyncratic reference systems as well as an analytic approximation to INDSCAL. Paper presented at the spring meeting of the Psychometric Society, Princeton, NJ.
Borg, I. and Shye, S., Facet Theory: form and content, Newbury Park, Sage, 1995.
Amat, L., Constans, P., BesalÚ, E. and Carbó-Dorca, R., MOLSIMIL 97, Institute of Computational Chemistry, University of Girona, Spain, 1997.
Constans, P. and Carbó, R., J. Chem. Inf. Comput. Sci., 35 (1995) 1046.
Amat, L. and Carbó-Dorca, R., J. Comput. Chem., 18 (1997) 2023.
ASA coefficients and exponents for an assorted sample of atoms can be seen and downloaded from the website: http://iqc.udg.es/cat/similarity/ASA/funcset.html
GiD, Geometry and Data, a pre/postprocessor graphical interface. It can be downloaded from the CIMNE website: http://gatxan.upc.es
All the steroid ASA isodensity plots shown in the paper can be seen and downloaded from: http://iqc.udg.es/cat/similarity/QSAR/facets/index.html
The steroid structures can be seen and downloaded from the Gasteiger' group Website: http://schiele.organik.unierlangen.de/services/steroids/
Gironés, X., Amat, L. and Carbó-Dorca, R., A comparative study of Isodensity surfaces using ab initio and ASA Density Functions. Technical Report: IT-IQC-98-30. J. Mol. Graph. Model, In press.
Watt, A. and Watt, M., Advanced Animation and Rendering Techniques, Addison-Wesley, London, 1992.
Lorensen, W.E. and Cline, H.E., Comput. Graphics, 21 (1987) 163.
Kaufman, L. and Rousseeuw, P.J., CLUSFIND software package. The code includes the PAM program used in this study, and it can be downloaded from the website: http://winwww.uia.ac.be/u/statis/programs.html
Dunn, J.F., Nisula, B.C. and Rodbard, D., J. Clin. Endocrinol. Metab., 53 (1981) 58.
Anzali, S., Barnickel, G., Krug, M., Sadowski, J., Wagener, M., Gasteiger, J. and Polanski, J., J. Comput.-Aided Mol. Design, 10 (1996) 521.
van Wezel, A.P. and Opperhuizen, A., Crit. Rev. Toxicol., 25 (1995) 255.
Cantor, R.S., Biochemistry, 36 (1997) 2339.
Van Leeeuwen, C.J., van der Zandt, P.T.J., Aldenberg, T., Verhaar, H.J.M. and Hermens, J.L.M., Environ. Toxicol. Chem., 11 (1992) 267.
Amat, L., Carbó-Dorca, R. and Ponec, R., J. Comput. Chem., 19 (1998) 1575.
Urrestarazu Ramos, E., Vermeer, C., Vaes, W.H.J. and Hermens, J.L.M., Chemosphere, 37 (1998) 633.
AMPAC 6.0, 1994 Semichem, 7128 Summit, Shawnee, KS 66216.D.A.
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Robert, D., Gironés, X. & Carbó-Dorca, R. Facet diagrams for quantum similarity data. J Comput Aided Mol Des 13, 597–610 (1999). https://doi.org/10.1023/A:1008039618288
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DOI: https://doi.org/10.1023/A:1008039618288