ReviewCurrent opinion in structural biology2013
To milliseconds and beyond: challenges in the simulation of protein folding.
Review in Current opinion in structural biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 148 papers.
What it found
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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.
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Who cites it
148 citing papers in PubMed.
- Multiscale frameworks for exploring protein energy landscapes: advances in theory and simulation.Journal of biological physics · 2026Review
- The Shape of Things to Come: α-Helical Membrane Protein Folding on the Ribosome.Chemical reviews · 2026Review
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- A Hydrophobic Cluster Modulates Long-Range Allostery in the TRMT2A RNA Recognition Motif.Journal of chemical information and modeling · 2026Article
- De novo Folding Mechanisms of Lasso Peptides.bioRxiv : the preprint server for biology · 2026Article
- Article
- The Role of the Electronic Structure during Protein Folding through Electron Density-Based Quantum Chemical Descriptors.ACS omega · 2026Article
- Resolving Molecular Interactions in Protein Folding Trajectories with NCIPLOT.Journal of chemical information and modeling · 2025Article
- Microbiota-derived corisin accelerates kidney fibrosis by promoting cellular aging.Nature communications · 2025Article
- Feasibility of Combining Biomolecular Conformational Sampling Techniques for Molecular Dynamics Simulation.Journal of computational chemistry · 2025Article
- The molecular mechanism of temperature-dependent phase separation of heat shock factor 1.Nature chemical biology · 2025Article
- Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies.The journal of physical chemistry. B · 2025Review
- Integrative spatiotemporal modeling of biomolecular processes: Application to the assembly of the nuclear pore complex.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Accuracy of Reaction Coordinate Based Rate Theories for Modelling Chemical Reactions: Insights From the Thermal Isomerization in Retinal.Journal of computational chemistry · 2025Article
- Molecular Crowding by Computational Approaches.Sub-cellular biochemistry · 2025Review
- Integrative spatiotemporal modeling of biomolecular processes: application to the assembly of the Nuclear Pore Complex.bioRxiv : the preprint server for biology · 2024Article
- Unveiling Conformational States of CDK6 Caused by Binding of Vcyclin Protein and Inhibitor by Combining Gaussian Accelerated Molecular Dynamics and Deep Learning.Molecules (Basel, Switzerland) · 2024Article
- Adsorption in Action: Molecular Dynamics as a Tool to Study Adsorption at the Surface of Fine Plastic Particles in Aquatic Environments.ACS omega · 2024Review
- One bead per residue can describe all-atom protein structures.Structure (London, England : 1993) · 2024Article
- Evaluations of FDA-approved Drugs Targeting 3CLP of SARS-CoV-2 Employing a Repurposing Strategy.Combinatorial chemistry & high throughput screening · 2024Article
88 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding have long been considered a holy grail of computational biology. Due to the large system sizes and long timescales involved, such a pursuit was for many years computationally intractable. Further, sufficiently accurate forcefields needed to be developed in order to realistically model folding. This decade, however, saw the first reports of folding simulations describing kinetics on the order of milliseconds, placing many proteins firmly within reach of these methods. Progress in sampling and forcefield accuracy, however, presents a new challenge: how to turn huge MD datasets into scientific understanding. Here, we review recent progress in MD simulation techniques and show how the vast datasets generated by such techniques present new challenges for analysis. We critically discuss the state of the art, including reaction coordinate and Markov state model (MSM) methods, and provide a perspective for the future.
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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.