ArticleJournal of chemical theory and computation2011
A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles.
Article in Journal of chemical theory and computation, 2011. 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.
- HP35 Protein in the Mesopore of MIL-101(Cr) MOF: A Model to Study Cotranslocational Unfolding.ACS omega · 2024Article
- Local Ion Densities can Influence Transition Paths of Molecular Binding.Frontiers in molecular biosciences · 2022Article
- Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale.Biophysical journal · 2020Article
- Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport.Nucleic acids research · 2019Article
- Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters.eLife · 2017Article
- The Origin of Coupled Chloride and Proton Transport in a ClJournal of the American Chemical Society · 2016Article
- Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter.Biophysical journal · 2016Article
- Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins.Journal of chemical theory and computation · 2016Article
- P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape.PLoS computational biology · 2014Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Convergence of Free Energy Profile of Coumarin in Lipid Bilayer.Journal of chemical theory and computation · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Free energy calculations are one of the most useful methods for the study of ion transport mechanisms through confined spaces such as protein ion channels. Their reliability depends on a correctly defined reaction coordinate (RC). A straight line is usually not a proper RC for such complicated processes so in this work a combined metadynamics/umbrella sampling (MTD/US) method is proposed. In the combined method, the ion transport pathway is first identified by the MTD method and then the free energy profile or potential of mean force (PMF) along the path is calculated using umbrella sampling. This combined method avoids the discontinuity problem often associated with normal umbrella sampling calculations that assume a straight line RC and it provides a more physically accurate PMF for such processes. The method is demonstrated for the proton transport process through the protein channel of aquaporin-1.
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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.