ArticleProtein science : a publication of the Protein Society2016
Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses.
Article in Protein science : a publication of the Protein Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias.Journal of chemical theory and computation · 2025Article
- A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis.Journal of chemical information and modeling · 2023Article
- Simulation of ligand dissociation kinetics from the protein kinase PYK2.Journal of computational chemistry · 2022Article
- Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature.Life (Basel, Switzerland) · 2022Article
- WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.Journal of chemical theory and computation · 2022Article
- What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models.Journal of chemical theory and computation · 2021Article
- Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" Analysis.Journal of chemical theory and computation · 2020Article
- Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping.Journal of chemical theory and computation · 2019Article
- Computational Estimation of Microsecond to Second Atomistic Folding Times.Journal of the American Chemical Society · 2019Article
- Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations.Chemical science · 2019Article
- NaPhysical chemistry chemical physics : PCCP · 2019Article
- Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.Annual review of biophysics · 2017Review
- Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models.Journal of chemical theory and computation · 2016Article
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4 authors.
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Abstract
First-passage times (FPTs) are widely used to characterize stochastic processes such as chemical reactions, protein folding, diffusion processes or triggering a stock option. In previous work (Suarez et al., JCTC 2014;10:2658-2667), we demonstrated a non-Markovian analysis approach that, with a sufficient subset of history information, yields unbiased mean first-passage times from weighted-ensemble (WE) simulations. The estimation of the distribution of the first-passage times is, however, a more ambitious goal since it cannot be obtained by direct observation in WE trajectories. Likewise, a large number of events would be required to make a good estimation of the distribution from a regular "brute force" simulation. Here, we show how the previously developed non-Markovian analysis can generate approximate, but highly accurate, FPT distributions from WE data. The analysis can also be applied to any other unbiased trajectories, such as from standard molecular dynamics simulations. The present study employs a range of systems with independent verification of the distributions to demonstrate the success and limitations of the approach. By comparison to a standard Markov analysis, the non-Markovian approach is less sensitive to the user-defined discretization of configuration space.
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