Mar 17, 2017

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

Annual Review of Biophysics
Daniel M Zuckerman, Lillian T Chong

Abstract

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.

  • References56
  • Citations20

References

Mentioned in this Paper

Computer Software
Molecular Dynamics
Gene Products, Protein
Computer Programs and Programming
Biophysics
Protein Conformation
Binding (Molecular Function)
Simulation
Protein Folding
Systems Biology

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