TOWARD A GLOBAL MAXIMIZATION OF THE MOLECULAR SIMILARITY FUNCTION - SUPERPOSITION OF 2 MOLECULES

A quantum similarity measure between two molecules is normally identif ied with the maximum value of the overlap of the corresponding molecul ar electron densities. The electron density overlap is a function of t he mutual positioning of the compared molecules, requiring the measure ment of similarity, a solution of a multiple-maxima problem. Collapsin g the molecular electron densities into the nuclei provides the essent ial information toward a global maximization of the overlap similarity function, the maximization of which, in this Limit case, appears to b e related to the so-called assignment problem. Three levels of approac h are then preposed for a global search scanning of the similarity fun ction. In addition, atom-atom similarity Lorentzian potential function s are defined for a rapid completion of the function scanning. Perform ance is tested among these three levels of simplification and the Mont e Carlo and simplex methods. Results reveal the present algorithms as accurate, rapid, and unbiased techniques for density-based molecular a lignments. (C) 1997 by John Wiley & Sons, Inc.