ArticleThe journal of physical chemistry. B2015
Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Cooperative Native Contact Formation Facilitates Free Energy Barrier Crossing in Protein Folding.Physical review letters · 2026Article
- Hierarchical friction memory leads to subdiffusive configurational dynamics of fast-folding proteins.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Fast protein folding is governed by memory-dependent friction.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation.Journal of chemical information and modeling · 2023Article
- Enhanced statistical sampling reveals microscopic complexity in the talin mechanosensor folding energy landscape.Nature physics · 2023Article
- Tuning Formation of Protein-DNA Coacervates by Sequence and Environment.The journal of physical chemistry. B · 2022Article
- Granger Causality Analysis of Chignolin Folding.Journal of chemical theory and computation · 2022Article
- Estimating transition path times and shapes from single-molecule photon trajectories: A simulation analysis.The Journal of chemical physics · 2021Article
- Learning dynamical information from static protein and sequencing data.Nature communications · 2019Article
- Diverse Folding Pathways of HIV-1 Protease Monomer on a Rugged Energy Landscape.Biophysical journal · 2019Article
- Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins.Physical chemistry chemical physics : PCCP · 2019Article
- Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force.The journal of physical chemistry. B · 2018Article
- Size and topology modulate the effects of frustration in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Transition Path Times Measured by Single-Molecule Spectroscopy.Journal of molecular biology · 2018Review
- Protein folding transition path times from single molecule FRET.Current opinion in structural biology · 2018Review
- Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N.PLoS computational biology · 2017Article
- Modulation of Folding Internal Friction by Local and Global Barrier Heights.The journal of physical chemistry letters · 2016Article
- Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Theoretical models have often modeled protein folding dynamics as diffusion on a low-dimensional free energy surface, a remarkable simplification. However, the accuracy of such an approximation and the number of dimensions required were not clear. For all-atom folding simulations of ten small proteins in explicit solvent we show that the folding dynamics can indeed be accurately described as diffusion on just a single coordinate, the fraction of native contacts (Q). The diffusion models reproduce both folding rates, and finer details such as transition-path durations and diffusive propagators. The Q-averaged diffusion coefficients decrease with chain length, as anticipated from energy landscape theory. Although the Q-diffusion model does not capture transition-path durations for the protein NuG2, we show that this can be accomplished by designing an improved coordinate Qopt. Overall, one-dimensional diffusion on a suitable coordinate turns out to be a remarkably faithful model for the dynamics of the proteins considered.
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.