ArticleThe Journal of chemical physics2021
The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations.
Article in The Journal of chemical physics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- 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
- 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
- Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry.Nature communications · 2022Article
- Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories.Journal of chemical information and modeling · 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
- The Next Frontier for Designing Switchable Proteins: Rational Enhancement of Kinetics.The journal of physical chemistry. B · 2021Article
- A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations.The journal of physical chemistry. A · 2021Article
- Weighted Ensemble Simulation: Advances in methods, software, and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We present the Rate from Event Durations (RED) scheme, a new scheme that more efficiently calculates rate constants using the weighted ensemble path sampling strategy. This scheme enables rate-constant estimation from shorter trajectories by incorporating the probability distribution of event durations, or barrier-crossing times, from a simulation. We have applied the RED scheme to weighted ensemble simulations of a variety of rare-event processes that range in complexity: residue-level simulations of protein conformational switching, atomistic simulations of Na
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Registered trials
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.