ArticleJournal of chemical theory and computation2015
Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- Unifying Single-Channel Permeability From Rare-Event Sampling and Steady-State Flux.Frontiers in molecular biosciences · 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
- Predicting pathological von Willebrand factor unraveling in elongational flow.Biophysical journal · 2021Article
- A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations.The journal of physical chemistry. A · 2021Article
- Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling.ACS omega · 2020Article
- Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" Analysis.Journal of chemical theory and computation · 2020Article
- Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations.Chemical science · 2019Article
- Molecular determination of claudin-15 organization and channel selectivity.The Journal of general physiology · 2018Article
- Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.Annual review of biophysics · 2017Review
- Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion Channels.The journal of physical chemistry. B · 2017Article
- Path-sampling strategies for simulating rare events in biomolecular systems.Current opinion in structural biology · 2017Review
- Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide.The journal of physical chemistry letters · 2016Article
- Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models.Journal of chemical theory and computation · 2016Article
- 15 Years of molecular simulation of drug-binding kinetics.Expert opinion on drug discoveryReview
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Ion channels are responsible for a myriad of fundamental biological processes via their role in controlling the flow of ions through water-filled membrane-spanning pores in response to environmental cues. Molecular simulation has played an important role in elucidating the mechanism of ion conduction, but connecting atomistically detailed structural models of the protein to electrophysiological measurements remains a broad challenge due to the computational cost of reaching the necessary time scales. Here, we introduce an enhanced sampling method for simulating the conduction properties of narrow ion channels using the Weighted ensemble (WE) sampling approach. We demonstrate the application of this method to calculate the current–voltage relationship as well as the nonequilibrium ion distribution at steady-state of a simple model ion channel. By direct comparisons with long brute force simulations, we show that the WE simulations rigorously reproduce the correct long-time scale kinetics of the system and are capable of determining these quantities using significantly less aggregate simulation time under conditions where permeation events are rare.
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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.