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Similarity measures based on Gaussian‐type promolecular electron density models: Alignment of small rigid molecules
Author(s) -
Leherte Laurence
Publication year - 2006
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20498
Subject(s) - similarity (geometry) , kinetic energy , gaussian , superposition principle , statistical physics , coulomb , graph , electron , work (physics) , mathematics , physics , biological system , computational chemistry , computer science , chemistry , classical mechanics , combinatorics , artificial intelligence , mathematical analysis , quantum mechanics , biology , image (mathematics)
Various molecular similarity measures (overlap, Coulomb, kinetic, electrostatic energy) and similarity indices (Carbó, Hodgkin–Richards, Kulczynski, Shape Tanimoto) are applied to the superposition of 3D promolecular electron density (PED) distributions. The original aspect of the paper lies in the consideration of smoothed PEDs, which allow to decrease the number of local solutions to a superposition problem, together with the use of the less common kinetic and electrostatic energy similarity measures. Results are obtained for a family of five rigid endothiapepsin ligands that were already considered in previous applications, based on graph representations of their PED. In the present work, it is observed that the use of smoothed PED and the kinetic similarity measure, together with the Kulczynski or Shape Tanimoto index, performed the best to align molecules of different sizes. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006