Although molecular dynamics (MD) simulations of biomolecules now routinely reach the microsecond timescale, biological phenomena typically occur on much longer timescales - e.g., folding, binding, and allosteric behavior.  Not only is it challenging to generate MD trajectories capturing these rare conformational processes, but also the analysis of such trajectories has remained surprisingly difficult.  Research progress on both fronts will be discussed, focusing on the weighted ensemble method for generating rare-event trajectories, along with unbiased variants of Markov state models for computing rates, populations, and mechanisms from trajectories.

Simulating and analyzing conformational processes in biomolecules

ACS Fall 2021

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