Oct 25, 2018

Reducing the impact of transient effects in rate-constant estimation using the weighted ensemble strategy

BioRxiv : the Preprint Server for Biology
Alex J. DeGrave, Lillian T Chong

Abstract

We present a new method for improving the efficiency of calculating rate constants using the weighted ensemble path sampling strategy. This method reduces the sensitivity of rate-constant estimation to the earliest (and least typical) pathways reaching the target state by incorporating the distribution of event durations (excluding dwell time in the initial stable state) that correspond to pathways captured by the simulation. We demonstrate that the improved method enables accurate estimation of the rate constant for a protein conformational switching process using a fraction of the simulation time required by the original weighted ensemble method. Importantly, our method accounts for systematic error when using data from the entire simulation. Our method is relevant to any simulation strategy that involves unbiased trajectories of similar length to the typical event duration, including weighted ensemble and standard simulations.

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Mentioned in this Paper

Biochemical Pathway
Macromolecular Alteration
Staphylococcal Protein A
Simulation

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