ArticleJournal of chemical theory and computation2016
Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modeling.Protein science : a publication of the Protein Society · 2025Review
- Supra-biological performance of immobilized enzymes enabled by chaperone-like specific non-covalent interactions.Nature communications · 2024Article
- Article
- Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms.Journal of chemical information and modeling · 2023Article
- A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis.Journal of chemical information and modeling · 2023Article
- Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials.The Journal of chemical physics · 2022Article
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
- Augmented transition path theory for sequences of events.The Journal of chemical physics · 2022Article
- Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature.Life (Basel, Switzerland) · 2022Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics.Nature communications · 2021Article
- What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models.Journal of chemical theory and computation · 2021Article
- Long-Time-Scale Predictions from Short-Trajectory Data: A Benchmark Analysis of the Trp-Cage Miniprotein.Journal of chemical theory and computation · 2021Article
- Article
- Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" Analysis.Journal of chemical theory and computation · 2020Article
- ivis Dimensionality Reduction Framework for Biomacromolecular Simulations.Journal of chemical information and modeling · 2020Article
- Sampling of the conformational landscape of small proteins with Monte Carlo methods.Scientific reports · 2020Article
- Integrated Variational Approach to Conformational Dynamics: A Robust Strategy for Identifying Eigenfunctions of Dynamical Operators.The journal of physical chemistry. B · 2020Article
- Deciphering the Allosteric Process of theThe journal of physical chemistry. B · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Because standard molecular dynamics (MD) simulations are unable to access time scales of interest in complex biomolecular systems, it is common to "stitch together" information from multiple shorter trajectories using approximate Markov state model (MSM) analysis. However, MSMs may require significant tuning and can yield biased results. Here, by analyzing some of the longest protein MD data sets available (>100 μs per protein), we show that estimators constructed based on exact non-Markovian (NM) principles can yield significantly improved mean first-passage times (MFPTs) for protein folding and unfolding. In some cases, MSM bias of more than an order of magnitude can be corrected when identical trajectory data are reanalyzed by non-Markovian approaches. The NM analysis includes "history" information, higher order time correlations compared to MSMs, that is available in every MD trajectory. The NM strategy is insensitive to fine details of the states used and works well when a fine time-discretization (i.e., small "lag time") is used.
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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.