ArticleJournal of the American Chemical Society2019
Computational Estimation of Microsecond to Second Atomistic Folding Times.
Article in Journal of the American Chemical Society, 2019. 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 41 papers.
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Who cites it
41 citing papers in PubMed.
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework.The journal of physical chemistry. A · 2026Article
- The Role of the Electronic Structure during Protein Folding through Electron Density-Based Quantum Chemical Descriptors.ACS omega · 2026Article
- Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly.Journal of chemical theory and computation · 2025Article
- Rapid estimation of protein folding pathways from sequence alone using AlphaFold2.Nature communications · 2025Article
- Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding.Journal of chemical theory and computation · 2025Article
- Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias.Journal of chemical theory and computation · 2025Article
- Analysis of the Dynamics of a Complex, Multipathway Reaction: Insulin Dimer Dissociation.The journal of physical chemistry. B · 2024Article
- Augmenting Human Expertise in Weighted Ensemble Simulations through Deep Learning-Based Information Bottleneck.Journal of chemical theory and computation · 2024Article
- Article
- Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRASJournal of chemical information and modeling · 2024Article
- BAD-NEUS: Rapidly converging trajectory stratification.The Journal of chemical physics · 2024Article
- AlphaFold2bioRxiv : the preprint server for biology · 2024Article
- WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.Journal of chemical information and modeling · 2024Article
- Revisiting Textbook Azide-Clock Reactions: A "Propeller-Crawling" Mechanism Explains Differences in Rates.Journal of the American Chemical Society · 2024Article
- Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein.Chemical science · 2024Article
- How Robust Is the Ligand Binding Transition State?Journal of the American Chemical Society · 2023Article
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.The international journal of high performance computing applications · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Despite the development of massively parallel computing hardware including inexpensive graphics processing units (GPUs), it has remained infeasible to simulate the folding of atomistic proteins at room temperature using conventional molecular dynamics (MD) beyond the microsecond scale. Here, we report the folding of atomistic, implicitly solvated protein systems with folding times τ ranging from ∼10 μs to ∼100 ms using the weighted ensemble (WE) strategy in combination with GPU computing. Starting from an initial structure or set of structures, WE organizes an ensemble of GPU-accelerated MD trajectory segments via intermittent pruning and replication events to generate statistically unbiased estimates of rate constants for rare events such as folding; no biasing forces are used. Although the variance among atomistic WE folding runs is significant, multiple independent runs are used to reduce and quantify statistical uncertainty. Folding times are estimated directly from WE probability flux and from history-augmented Markov analysis of the WE data. Three systems were examined: NTL9 at low solvent viscosity (yielding τ
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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.