ArticleProceedings of the National Academy of Sciences of the United States of America2013
Atomic-level description of ubiquitin folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 137 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
137 citing papers in PubMed, 338 citations in OpenAlex.
- Signatures of protein fold switching in the unfolded state.Biophysical journal · 2026Article
- Adaptive Tensor Train Metadynamics for High-Dimensional Free Energy Exploration.Journal of chemical theory and computation · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Cosolutes Modulate Polyubiquitin Fibrillation.ACS omega · 2026Article
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- Beyond Classical Force Fields: Physics-Driven Assessment of the Grappa Machine-Learned Force Field on the FoldBind Dataset.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Learning data-efficient coarse-grained molecular dynamics from forces and noise.Nature communications · 2026Article
- Automatic forward model parameterization with Bayesian inference of conformational populations.APL machine learning · 2026Article
- The Role of the Electronic Structure during Protein Folding through Electron Density-Based Quantum Chemical Descriptors.ACS omega · 2026Article
- Protein language models trained on biophysical dynamics inform mutation effects.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Rapid estimation of protein folding pathways from sequence alone using AlphaFold2.Nature communications · 2025Article
- Optimized protein-water interactions and torsional refinements yield balanced atomistic protein force fields.Nature communications · 2025Article
- Structure of a transient protein-folding intermediate by pressure-jump NMR spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.The journal of physical chemistry letters · 2025Article
- Non-native entanglement protein misfolding observed in all-atom simulations and supported by experimental structural ensembles.Science advances · 2025Article
- Automatic Forward Model Parameterization with Bayesian Inference of Conformational Populations.ArXiv · 2025Article
- Application of Anomaly Detection to Identify Important Features of Protein Dynamics.ACS omega · 2025Article
- An integrative characterization of proline cis and trans conformers in a disordered peptide.Biophysical journal · 2024Article
- AbMelt: Learning antibody thermostability from molecular dynamics.Biophysical journal · 2024Article
- AlphaFold2bioRxiv : the preprint server for biology · 2024Article
77 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Equilibrium molecular dynamics simulations, in which proteins spontaneously and repeatedly fold and unfold, have recently been used to help elucidate the mechanistic principles that underlie the folding of fast-folding proteins. The extent to which the conclusions drawn from the analysis of such proteins, which fold on the microsecond timescale, apply to the millisecond or slower folding of naturally occurring proteins is, however, unclear. As a first attempt to address this outstanding issue, we examine here the folding of ubiquitin, a 76-residue-long protein found in all eukaryotes that is known experimentally to fold on a millisecond timescale. Ubiquitin folding has been the subject of many experimental studies, but its slow folding rate has made it difficult to observe and characterize the folding process through all-atom molecular dynamics simulations. Here we determine the mechanism, thermodynamics, and kinetics of ubiquitin folding through equilibrium atomistic simulations. The picture emerging from the simulations is in agreement with a view of ubiquitin folding suggested from previous experiments. Our findings related to the folding of ubiquitin are also consistent, for the most part, with the folding principles derived from the simulation of fast-folding proteins, suggesting that these principles may be applicable to a wider range of proteins.
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.