ArticleJournal of chemical theory and computation2020
Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" Analysis.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 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
- Augmenting Human Expertise in Weighted Ensemble Simulations through Deep Learning-Based Information Bottleneck.Journal of chemical theory and computation · 2024Article
- Article
- BAD-NEUS: Rapidly converging trajectory stratification.The Journal of chemical physics · 2024Article
- WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.Journal of chemical information and modeling · 2024Article
- Force-regulated chaperone activity of BiP/ERdj3 is opposite to their homologs DnaK/DnaJ.Protein science : a publication of the Protein Society · 2024Article
- How Robust Is the Ligand Binding Transition State?Journal of the American Chemical Society · 2023Article
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].Living journal of computational molecular science · 2023Article
- #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.The international journal of high performance computing applications · 2023Article
- Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics.Chemical science · 2022Article
- Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry.Nature communications · 2022Article
- WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.Journal of chemical theory and computation · 2022Article
- Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling.Journal of chemical theory and computation · 2021Article
- #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol.bioRxiv : the preprint server for biology · 2021Article
- A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications.American journal of physics · 2021Article
- The Next Frontier for Designing Switchable Proteins: Rational Enhancement of Kinetics.The journal of physical chemistry. B · 2021Article
- The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.Briefings in bioinformatics · 2021Review
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2 authors.
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Abstract
The weighted ensemble (WE) simulation strategy provides unbiased sampling of nonequilibrium processes, such as molecular folding or binding, but the extraction of rate constants relies on characterizing steady-state behavior. Unfortunately, WE simulations of sufficiently complex systems will not relax to steady state on observed simulation times. Here, we show that a postsimulation clustering of molecular configurations into "microbins" using methods developed in the Markov State Model (MSM) community can yield unbiased kinetics from WE data before steady-state convergence of the WE simulation itself. Because WE trajectories are directional and not equilibrium distributed, the history-augmented MSM (haMSM) formulation can be used, which yields the mean first-passage time (MFPT) without bias for arbitrarily small lag times. Accurate kinetics can be obtained while bypassing the often prohibitive convergence requirements of the nonequilibrium weighted ensemble. We validate the method in a simple diffusive process on a two-dimensional (2D) random energy landscape and then analyze atomistic protein folding simulations using WE molecular dynamics. We report significant progress toward the unbiased estimation of protein folding times and pathways, though key challenges remain.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.