Abstract
Fragment-based methods for drug optimization have great potential; however, time, expense and sensitivity considerations associated with NMR and x-ray crystallographic based methods limit their applicability. As an alternative we have developed a computational approach, SILCS: Site Identification by Ligand Competitive Saturation, that uses explicit solvent all-atom molecular dynamics to identify binding sites on protein surfaces for functional groups. Information from the SILCS approach may then be combined with structural information on an inhibitor-protein complex to facilitate modification of the ligand to improve its binding affinity. An overview of SILCS and its application to inhibitor-ligand optimization will be presented.
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