Abstract
This chapter gives an overview of currently available free energy (FE) methods to support the optimization of ligand binding to protein targets. The calculations provide insights into the physical chemistry of protein–ligand interactions and can be used as a practical tool to optimize initial hit compounds during drug discovery. After a broad introduction to these methods, the techniques are reviewed with particular emphasis on their use in the lead optimization (LO) phase of drug discovery. Besides providing examples which are of pharmaceutical interest, it also gives practical suggestions on the choice of an FE method and best practices.
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