Calculating binding free energies from molecular
simulations: Blind predictions, model binding sites, and automated planning

I discuss work in alchemical free energy calculations based on molecular
simulations, and their application in blind predictions in a series of
different model binding sites. This work provides a variety of insights into
protein-ligand binding, the accuracy of force fields, and the importance of
even relatively small conformational changes. I also discuss ongoing work
automating free energy calculations for applications to the lead optimization
phase of pharmaceutical drug discovery.