Abstract:Accurate and efficient simulation of the thermodynamics and kinetics of protein-ligand interactions is crucial for computational drug discovery. Multiensemble Markov Model (MEMM) estimators can provide estimates of both binding rates and affinities from collections of short trajectories, but have not been systematically explored for situations when a ligand is decoupled through scaling of non-bonded interactions. In this work, we compare the performance of two MEMM approaches for estimating ligand binding affi… Show more
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