In this talk, I will cover highlights from our recent work in the area of predicting protein-ligand interactions using molecular simulations and binding free energy calculations. This will include insights into protein motions and protein conformational changes from recent work with equilibrium and nonequilibrium binding free energy calculations, as well as work on the role of water rearrangement and water sampling around protein binding sites. We also discuss how comparison with electron density maps derived from X-ray crystallography can provide additional insight beyond that obtained from comparing to deposited crystallographic structures. A particular focus will be on lessons learned.

Challenges facing binding free energy calculations for molecular design

ACS Fall 2021

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