%0 Journal Article %1 Zuckerman2017WEReview %A Zuckerman, Daniel M. %A Chong, Lillian T. %D 2017 %J Annual Review of Biophysics %K enhanced-sampling molecular-dynamics weighted-ensemble %N 1 %P 43-57 %R 10.1146/annurev-biophys-070816-033834 %T Weighted Ensemble Simulation: Review of Methodology, Applications, and Software %U http://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-070816-033834 %V 46 %X 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. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

@article{Zuckerman2017WEReview, 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. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates. }, added-at = {2017-03-31T23:16:21.000+0200}, author = {Zuckerman, Daniel M. and Chong, Lillian T.}, biburl = {https://www.bibsonomy.org/bibtex/23ccdff53e4eb4cf79376e677e93ced63/salotz}, description = {Weighted Ensemble Simulation: Review of Methodology, Applications, and Software | Annual Review of Biophysics}, doi = {10.1146/annurev-biophys-070816-033834}, eprint = {http://dx.doi.org/10.1146/annurev-biophys-070816-033834}, interhash = {e3f19b2245f78acf64ad8bda82cb987d}, intrahash = {3ccdff53e4eb4cf79376e677e93ced63}, journal = {Annual Review of Biophysics}, keywords = {enhanced-sampling molecular-dynamics weighted-ensemble}, note = {PMID: 28301772}, number = 1, pages = {43-57}, timestamp = {2017-08-10T04:55:22.000+0200}, title = {Weighted Ensemble Simulation: Review of Methodology, Applications, and Software}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-070816-033834}, volume = 46, year = 2017 }