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| - Superposition of Three-Dimensional Chemical Structures Allowing for ConformationalFlexibility by a Hybrid Method
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| - The superposition of three-dimensional structures is the firsttask in the evaluation of the largest commonthree-dimensional substructure of a set of molecules. This is animportant step in the identification of apharmacophoric pattern for molecules that bind to the same receptor.The superposition method describedhere combines a genetic algorithm with a numerical optimization method.A major goal is to adequatelyaddress the conformational flexibility of ligand molecules. Thegenetic algorithm optimizes in anondeterministic process the size and the geometric fit of thesubstructures. The geometric fit is furtherimproved by changing torsional angles combining the genetic algorithmand the directed tweak method.This directed tweak method is based on a numerical quasi-Newtonoptimization method. Only one startingconformation per molecule is necessary. Molecules having severalrotatable bonds and quite different initialconformations are modified to find large structural similarities.A set of angiotensin II antagonists isinvestigated to illustrate the performance of the method.
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