Similarity measures: Is it possible to compare dissimilar structures?

Journal of Chemical Information and Computer Sciences

Volumn 38, Issue 4, 1998, Pages 691-701

  Sello, Guido ^a  

^a UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0013078997     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci980180k     Document Type: Article

References (21)

1. Concepts and Applications of Molecular Similarity; Johnson, M. A., Maggiora, G. M., Eds.; Wiley Interscience: New York, 1990.
2. Molecular Similarity and Reactivity: From Quantum Chemical to Phenomenological Approaches; Carbó, R., Ed.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1995.
3. Advances in Molecular Similarity; Carbó-Dorca, R., Mezey, P. G., Eds.; JAI Press Inc.: London, 1996.
4. Bath, P. A.; Poirrette, A. R.; Willett, P.; Allen, F. H. J. Chem. Inf. Comput. Sci. 1994, 34, 141-147.
5. Judson, P. N. J. Chem. Inf. Comput. Sci. 1994, 34, 148-153.
6. For some commercial packages using molecular similarity: (a) Grethe, G.; Moock, T. E. J. Chem. Inf. Comput. Sci. 1990, 30, 511-520. (b) Grethe, G.; Hounshell, W. D. In Chemical Structures 2. Proceedings of the 2nd International Conference, 1990; Warr, W. A., Ed.; Springer-Verlag: Berlin, 1993; pp 399-407.
7. For some commercial packages using molecular similarity: (a) Grethe, G.; Moock, T. E. J. Chem. Inf. Comput. Sci. 1990, 30, 511-520. (b) Grethe, G.; Hounshell, W. D. In Chemical Structures 2. Proceedings of the 2nd International Conference, 1990; Warr, W. A., Ed.; Springer-Verlag: Berlin, 1993; pp 399-407.
8. Benigni, R.; Andreoli, C.; Giuliani, A. Environ. Mol. Mutagen. 1994, 24, 208-219.
9. Martin, E. J.; Blaney, J. M.; Siani, M. A.; Spellmeyer, D. C.; Wong, A. K.; Moos, W. H. J. Med. Chem. 1995, 38, 1431-1436.
10. McGregor, M. J.; Pallai, P. V. J. Chem. Inf. Comput. Sci. 1997, 37, 443-448.
11. Lewis, R. A.; Mason, J. S.; McLay, I. M. J. Chem. Inf. Comput. Sci. 1997, 37, 599-614.
12. Agrafiotis, D. K. J. Chem. Inf. Comput. Sci. 1997, 37, 841-851.
13. Gillet, V. J.; Willet, P.; Bradshaw, J. J. Chem. Inf. Comput. Sci. 1997, 37, 731-740.
14. Sello, G.; Termini, M. Tetrahedron 1997, 53, 3729-3756.
15. Basak, S. C. 7th Conference on Mathematical Chemistry, Girona, Spain, 1996.
16. Sello, G.; Termini, M. In Advances in Molecular Similarity; Carbó-Dorca, R., Mezey, P. G., Eds.; JAI Press Inc.: London, 1996; pp 213-242.
17. i are the shell occupation numbers.
18. Mechanism of W calculation is based on a very simple idea: if we think that the electronic energy of a molecule is in relation with the energy of its atoms as result from their reciprocal interactions, we can affirm that the presence/absence of an atom in a specific position determines an energetic variation which can be thought of as the quantification of the difference between that molecule and a hypothetical molecule where that atom is isolated (annihilation principle). Therefore if we consider two identical molecules and we work on atoms in complete correspondences the energy variation will be identical; on the contrary, if we consider two different molecules and we work on similar atoms or if we consider two identical molecules and we work on different atoms, the calculated energy differences will be different and they will represent a measure of the "importance" of the atom in the molecule. Thus, we have available a similarity measure that, comparing the energy variations corresponding to specific substructures, evaluates the degree of their similarity.
19. i is the number of compounds of the TS used to describe A and B.
20. i is the number of similar atoms in fragment i and A and B are the total numbers of atoms of molecules A and B.
21. Sello, G.; Termini, M. In Advances in Molecular Similarity; Carbó-Dorca, R., Mezey, P. G., Eds.; JAI Press Inc.: London, 1996; pp 243-266.