ArticleThe Journal of chemical physics2008
Comment on "Free energy simulations of single and double ion occupancy in gramicidin A" [J. Chem. Phys. 126, 105103 (2007)].
Article in The Journal of chemical physics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- A claudin5-binding peptide enhances the permeability of the blood-brain barrier in vitro.Science advances · 2025Article
- Quantitative insights into the mechanism of proton conduction and selectivity for the human voltage-gated proton channel Hv1.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Calcium-gated potassium channel blockade via membrane-facing fenestrations.Nature chemical biology · 2024Article
- Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory.The journal of physical chemistry. B · 2021Article
- Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.Journal of chemical theory and computation · 2021Article
- Bases of Bacterial Sodium Channel Selectivity Among Organic Cations.Scientific reports · 2019Article
- The Origin of Coupled Chloride and Proton Transport in a ClJournal of the American Chemical Society · 2016Article
- Article
- Funnel metadynamics as accurate binding free-energy method.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT.Biophysical journal · 2012Article
- Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations.The journal of physical chemistry. B · 2011Article
- Making structural sense of dimerization interfaces of delta opioid receptor homodimers.Biochemistry · 2011Article
- Energetics of double-ion occupancy in the gramicidin A channel.The journal of physical chemistry. B · 2010Article
- Lessons from free energy simulations of delta-opioid receptor homodimers involving the fourth transmembrane helix.Biochemistry · 2010Article
- Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information.The Journal of chemical physics · 2009Article
- Computations of standard binding free energies with molecular dynamics simulations.The journal of physical chemistry. B · 2009Review
Corrections and comments
- Comment on
Authors and funding
3 authors.
Funding
Abstract
In a recent article published by Bastug and Kuyucak [J. Chem. Phys.126, 105103 (2007)] investigated the microscopic factors affecting double ion occupancy in the gramicidin channel. The analysis relied largely on the one-dimensional potential of mean force of ions along the axis of the channel (the so-called free energy profile of the ion along the channel axis), as well as on the calculation of the equilibrium association constant of the ions in the channel binding sites. It is the purpose of this communication to clarify this issue.
Indexed as
Identifiers
What OpenQuestion holds
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.