ArticleEntropy (Basel, Switzerland)2017
Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning.
Article in Entropy (Basel, Switzerland), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Survival strategies of artificial active agents.Scientific reports · 2023Article
- ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.Journal of chemical theory and computation · 2022Article
- Computing transition path theory quantities with trajectory stratification.The Journal of chemical physics · 2022Article
- Method for Identifying Common Features in Reactive Trajectories of a Transition Path Sampling Ensemble.Journal of chemical theory and computation · 2022Article
- Peptide Permeation across a Phosphocholine Membrane: An Atomically Detailed Mechanism Determined through Simulations and Supported by Experimentation.The journal of physical chemistry. B · 2022Article
- Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning.The journal of physical chemistry. B · 2021Article
- Long-Time-Scale Predictions from Short-Trajectory Data: A Benchmark Analysis of the Trp-Cage Miniprotein.Journal of chemical theory and computation · 2021Article
- Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations.Entropy (Basel, Switzerland) · 2021Article
- Data-driven reaction coordinate discovery in overdamped and non-conservative systems: application to optical matter structural isomerization.Nature communications · 2021Article
- Catalytic Magnesium as a Door Stop for DNA Sliding.The journal of physical chemistry. B · 2021Article
- Value of Temporal Information When Analyzing Reaction Coordinates.Journal of chemical theory and computation · 2020Article
- Milestoning with wind: Exploring the impact of a biasing potential in exact calculation of kinetics.The Journal of chemical physics · 2020Article
- The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning.Biochimica et biophysica acta. General subjects · 2020Article
- ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory.Journal of chemical theory and computation · 2020Article
- Defect-Assisted Permeation Through a Phospholipid Membrane: Experimental and Computational Study of the Peptide WKW.The journal of physical chemistry. B · 2019Article
- Ion Permeation through a Phospholipid Membrane: Transition State, Path Splitting, and Calculation of Permeability.Journal of chemical theory and computation · 2019Article
- Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere?Entropy (Basel, Switzerland) · 2018Article
- Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.The Journal of chemical physics · 2017Article
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5 authors.
Funding
Abstract
Reaction coordinates are vital tools for qualitative and quantitative analysis of molecular processes. They provide a simple picture of reaction progress and essential input for calculations of free energies and rates. Iso-committor surfaces are considered the optimal reaction coordinate. We present an algorithm to compute efficiently a sequence of isocommittor surfaces. These surfaces are considered an optimal reaction coordinate. The algorithm analyzes Milestoning results to determine the committor function. It requires only the transition probabilities between the milestones, and not transition times. We discuss the following numerical examples: (i) a transition in the Mueller potential; (ii) a conformational change of a solvated peptide; and (iii) cholesterol aggregation in membranes.
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