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Toward a global maximization of the molecular similarity function: Superposition of two molecules
Author(s) -
Constans Pere,
Amat Lluís,
CarbóDorca Ramon
Publication year - 1997
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/(sici)1096-987x(19970430)18:6<826::aid-jcc8>3.0.co;2-u
Subject(s) - similarity (geometry) , maxima and minima , maximization , simplex , statistical physics , electron density , function (biology) , limit (mathematics) , atom (system on chip) , chemistry , mathematics , electron , physics , computer science , quantum mechanics , mathematical optimization , combinatorics , image (mathematics) , artificial intelligence , mathematical analysis , evolutionary biology , biology , embedded system
A quantum similarity measure between two molecules is normally identified with the maximum value of the overlap of the corresponding molecular electron densities. The electron density overlap is a function of the mutual positioning of the compared molecules, requiring the measurement of similarity, a solution of a multiple‐maxima problem. Collapsing the molecular electron densities into the nuclei provides the essential information toward a global maximization of the overlap similarity function, the maximization of which, in this limit case, appears to be related to the so‐called assignment problem. Three levels of approach are then proposed for a global search scanning of the similarity function. In addition, atom—atom similarity Lorentzian potential functions are defined for a rapid completion of the function scanning. Performance is tested among these three levels of simplification and the Monte Carlo and simplex methods. Results reveal the present algorithms as accurate, rapid, and unbiased techniques for density‐based molecular alignments. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 826–846, 1997