ArticleThe Journal of chemical physics2012
An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates.
Article in The Journal of chemical physics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling.Journal of chemical theory and computation · 2023Article
- Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv : the preprint server for biology · 2023Article
- Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.Annual review of biophysics · 2017Review
- Markov State Models of gene regulatory networks.BMC systems biology · 2017Article
- WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis.Journal of chemical theory and computation · 2015Article
- Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.Journal of chemical theory and computation · 2014Article
- WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm.The journal of physical chemistry. B · 2014Article
- Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model.PLoS computational biology · 2014Article
- Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.The Journal of chemical physics · 2013Article
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2 authors.
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Abstract
We introduce an adaptive weighted-ensemble procedure (aWEP) for efficient and accurate evaluation of first-passage rates between states for two-state systems. The basic idea that distinguishes aWEP from conventional weighted-ensemble (WE) methodology is the division of the configuration space into smaller regions and equilibration of the trajectories within each region upon adaptive partitioning of the regions themselves into small grids. The equilibrated conditional∕transition probabilities between each pair of regions lead to the determination of populations of the regions and the first-passage times between regions, which in turn are combined to evaluate the first passage times for the forward and backward transitions between the two states. The application of the procedure to a non-trivial coarse-grained model of a 70-residue calcium binding domain of calmodulin is shown to efficiently yield information on the equilibrium probabilities of the two states as well as their first passage times. Notably, the new procedure is significantly more efficient than the canonical implementation of the WE procedure, and this improvement becomes even more significant at low temperatures.
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