ArticleThe Journal of chemical physics2013
Catch bond-like kinetics of helix cracking: network analysis by molecular dynamics and milestoning.
Article in The Journal of chemical physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. 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.
- Theory and Examples of Catch Bonds.The journal of physical chemistry. B · 2024Article
- Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning.The journal of physical chemistry. B · 2021Article
- Unraveling the mechanism of the cadherin-catenin-actin catch bond.PLoS computational biology · 2018Article
- Molecular mechanics of coiled coils loaded in the shear geometry.Chemical science · 2018Article
- Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning.The journal of physical chemistry. B · 2016Article
- Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning.Journal of computational chemistry · 2016Article
- Perspective: Computer simulations of long time dynamics.The Journal of chemical physics · 2016Article
- Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.PLoS computational biology · 2015Article
- Exact milestoning.The Journal of chemical physics · 2015Article
- Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.The Journal of chemical physics · 2015Article
- Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.The Journal of chemical physics · 2014Article
- Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Computational study of peptide permeation through membrane: Searching for hidden slow variables.Molecular physics · 2013Article
- RaTrav: a tool for calculating mean first-passage times on biochemical networks.BMC systems biology · 2013Article
- Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples.The Journal of chemical physics · 2013Article
- Perspective: Reaches of chemical physics in biology.The Journal of chemical physics · 2013Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
The first events of unfolding of secondary structure under load are considered with Molecular Dynamics simulations and Milestoning analysis of a long helix (126 amino acids). The Mean First Passage Time is a non-monotonic function of the applied load with a maximum of 3.6 ns at about 20 pN. Network analysis of the reaction space illustrates the opening and closing of an off-pathway trap that slows unfolding at intermediate load levels. It is illustrated that the nature of the reaction networks changes as a function of load, demonstrating that the process is far from one-dimensional.
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.