Putting molecular similarity into context: Asymmetric indices for field-based similarity measures

Journal of Mathematical Chemistry

Volumn 39, Issue 1, 2006, Pages 107-118

  Mestres, Jordi ^a   Maggiora, Gerald M ^b  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b UNIVERSITY OF ARIZONA   (United States)

Author keywords

Asymmetric similarity; Molecular fields; Similarity searching; Virtual screening

Indexed keywords

EID: 33644853942     PISSN: 02599791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10910-005-9007-3     Document Type: Article

References (18)

1. A. Tversky, Features of similarity, Psychol. Rev. 84 (1977) 327-352.
2. E.W. Holman, Monotonic models for asymmetric proximities, J. Math. Psychol. 20 (1979) 1-15.
3. R.M. Nosofsky, Stimulus bias, asymmetric similarity, and classification, Cogn. Psychol. 23 (1991) 91-140.
4. M. Johannesson, Modelling asymmetric similarity with prominence, Br. J. Math. Stat. Psychol. 53 (2000) 121-139.
5. G.M. Maggiora and V. Shanmugasundaram, Molecular Similarity Measures, in Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery, ed. J. Bajorath, Methods Mol Biol., vol. 275, pp. 1-50.
6. P. Willett, Chemical similarity searching, J. Chem. Inf. Comput. Sci. 38 (1998) 983-996.
7. J. Bradshaw, Introduction to Tversky similarity measure. Presented at the 11th Annual Daylight MUG Meeting, Laguna Beach (CA), February 1997. http://www.daylight.com/meetings/mug97/Bradshaw/MUG97/tv_tversky.html.
8. G.M. Maggiora, J. Mestres, T.R. Hagadone and M.S. Lajiness, Asymmetric similarity and molecular diversity, Presented at the 213th National Meeting of the American Chemical Society, San Francisco (CA), April 1997.
9. J.D. Holliday, N. Salim, M. Whittle and P. Willett, Analysis and display of the size dependence of chemical similarity coefficients, J. Chem. Inf. Comput. Sci. 43 (2003) 819-828.
10. R.D. Cramer III, D.E. Patterson and J.D. Bunce, Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins, J. Am. Chem. Soc. 110 (1988) 5959-5967.
11. G. Klebe, U. Abraham and T. Mietzner, Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity, J. Med. Chem. 37 (1994) 4130-4146.
12. C. Lemmen and T. Lengauer, Computational methods for the structural alignment of molecules, J. Comput. Aided Mol. Design 14 (2000) 215-232.
13. R. Carbó, E. Besalú, L. Amat and X. Fradera, On quantum molecular similarity measures (QMSM) and indices (QMSI), J. Math. Chem. 19 (1996) 47-56.
14. G.M. Maggiora, J.D. Petke and J. Mestres, A general analysis of field-based molecular similarity indices, J. Math. Chem. 31 (2002) 251-270.
15. R. Carbó, L. Leyda and M. Arnau, How similar is a molecule to another? An electron density measure of similarity between two molecular structures, Intl. J. Quantum Chem. 17 (1980) 1185-1189.
16. E.E. Hodgkin and W.G. Richards, Molecular similarity based on electrostatic potential and electric field, Intl. J. Quantum Chem. Quantum Biol. Symp. 14 (1987) 105-110.
17. J.D. Petke, Cumulative and discrete similarity analysis of electrostatic potentials and fields, J. Comput. Chem. 14 (1993) 928-933.
18. G.J. Klir and B. Yuan, Fuzzy Sets and Fuzzy Logic - Theory and Applications (Prentice-Hall, Upper Saddle River, NJ, 1995) Chapter 3.