ArticleProceedings of the National Academy of Sciences of the United States of America2012
Simple few-state models reveal hidden complexity in protein folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
- A Simulation-Free Topological Basis for Building Compact Koopman Models of Protein Folding.Journal of chemical information and modeling · 2026Article
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- Random Functions as Data Compressors for Machine Learning of Molecular Processes.Journal of chemical theory and computation · 2026Article
- The Role of the Electronic Structure during Protein Folding through Electron Density-Based Quantum Chemical Descriptors.ACS omega · 2026Article
- 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
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Exploring force-driven stochastic folding dynamics in mechano-responsive proteins and implications in phenotypic variation.Nature communications · 2025Article
- Article
- A Study of a Protein-Folding Machine: Transient Rotation of the Polypeptide Backbone Facilitates Rapid Folding of Protein Domains in All-Atom Molecular Dynamics Simulations.International journal of molecular sciences · 2023Article
- Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation.Journal of chemical information and modeling · 2023Article
- Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes.Frontiers in molecular biosciences · 2023Article
- GraphVAMPNet, using graph neural networks and variational approach to Markov processes for dynamical modeling of biomolecules.The Journal of chemical physics · 2022Article
- Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories.Journal of chemical theory and computation · 2022Article
- Phospholipid Scrambling by G Protein-Coupled Receptors.Annual review of biophysics · 2022Review
- Mechanistic Kinetic Model Reveals How Amyloidogenic Hydrophobic Patches Facilitate the Amyloid-β Fibril Elongation.ACS chemical neuroscience · 2022Article
- Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain.Scientific reports · 2022Article
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- The Two-Step Clustering Approach for Metastable States Learning.International journal of molecular sciences · 2021Review
- Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2.Journal of chemical information and modeling · 2021Article
- CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles.Bioinformatics (Oxford, England) · 2021Article
17 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Markov state models constructed from molecular dynamics simulations have recently shown success at modeling protein folding kinetics. Here we introduce two methods, flux PCCA+ (FPCCA+) and sliding constraint rate estimation (SCRE), that allow accurate rate models from protein folding simulations. We apply these techniques to fourteen massive simulation datasets generated by Anton and Folding@home. Our protocol quantitatively identifies the suitability of describing each system using two-state kinetics and predicts experimentally detectable deviations from two-state behavior. An analysis of the villin headpiece and FiP35 WW domain detects multiple native substates that are consistent with experimental data. Applying the same protocol to GTT, NTL9, and protein G suggests that some beta containing proteins can form long-lived native-like states with small register shifts. Even the simplest protein systems show folding and functional dynamics involving three or more states.
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