Multiple-Start Monte Carlo Docking of Flexible Ligands
The docking problem has received a great deal of attention over the last few years, with the appearance of a number of automated docking methods. These methods can be divided into two classes: shape-based methods, which use a simplified representation of the molecular surfaces as a means to guide docking, and energy-based methods, which search for good dockings based on favorable interaction energy. Each type of approach has its advantages and disadvantages. We give a detailed presentation of our method, which is essentially a combination of shape-based and energybased approaches, and uses the method of simulated annealing to optimize dockings. We also present a recent study that examines a new approach to the problem of dealing with flexible ligands.
KeywordsSimulated Annealing Binding Mode Docking Method Docking Procedure Flexible Ligand
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