ArticleJournal of computational chemistry2015
Accelerated molecular dynamics simulations of protein folding.
Article in Journal of computational chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- A Quantum-Classical Analysis of Variability in Peptide Energies and Conformations.The protein journal · 2026Article
- E50A Mutation Increases the Bioluminescence Activity of picALuc.Biosensors · 2026Article
- Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework.The journal of physical chemistry. A · 2026Article
- Advances in Computational Modeling and Machine Learning of Cellulosic Biopolymers: A Comprehensive Review.Biomimetics (Basel, Switzerland) · 2025Review
- Article
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- Prediction of aggregation in monoclonal antibodies from molecular surface curvature.Scientific reports · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Exploring the Anticancer Potential of Furanpydone A: A Computational Study on its Inhibition of MTHFD2 Across Diverse Cancer Cell Lines.Cell biochemistry and biophysics · 2025Article
- Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations.Computational and structural biotechnology journal · 2025Article
- Molecular Mechanisms Involved in the B Cell Growth and Clonogenic Activity of HIV-1 Matrix Protein p17 Variants.Viruses · 2024Article
- Illuminating ligand-induced dynamics in nuclear receptors through MD simulations.Biochimica et biophysica acta. Gene regulatory mechanisms · 2024Review
- Conformational analysis of the IQSEC2 protein by statistical thermodynamics.Current research in structural biology · 2024Article
- Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters.Mini reviews in medicinal chemistry · 2024Review
- Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations.Journal of chemical information and modeling · 2023Article
- Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein.ACS omega · 2023Article
- Functionalized Fullerene Potentially Inhibits SARS-CoV-2 Infection by Modulating Spike Protein Conformational Changes.International journal of molecular sciences · 2023Article
- Application of Molecular Dynamics Simulations to Determine Interactions between Canary Seed (International journal of molecular sciences · 2023Article
- Deep Boosted Molecular Dynamics: Accelerating Molecular Simulations with Gaussian Boost Potentials Generated Using Probabilistic Bayesian Deep Neural Network.The journal of physical chemistry letters · 2023Article
- Deep Boosted Molecular Dynamics (DBMD): Accelerating molecular simulations with Gaussian boost potentials generated using probabilistic Bayesian deep neural network.bioRxiv : the preprint server for biology · 2023Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.
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Registered trials
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