Abstract
Typical molecular dynamics (MD) simulations do not reach equilibrium and hence their trajectory data do not correspond to a well-defined statistical distribution. On the other hand, multiple trajectories initiated from the same configuration can be averaged to yield well-defined, time-dependent properties. This strategy can be implemented using conventional MD or the weighted ensemble (WE) approach. We apply both methods to study the conformational dynamics of the ligand binding domain of estrogen receptor alpha in several settings - the wild-type and two mutants important in metastatic breast cancer, as well as apo and ligand-bound conditions. Overall, the simulations enable us to make quantitative determinations of when the conformational behavior is statistically distinguishable under the various conditions.
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