ArticleNature communications2021
Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- Stable simulations do not guarantee functional engagement: a case study of off-target prediction for Seladelpar and Zanamivir.Journal of computer-aided molecular design · 2026Article
- Virtual Screening of Bacteriocins From Lactic Acid Bacteria Against Monkeypox DNA Polymerase: Sakacin P and Mundticin KS Emerge as Promising Candidates.Food science & nutrition · 2026Article
- Functional Analysis of a Novel Pathogenic Glycine Amidinotransferase Mutant in Hereditary Fanconi Syndrome.Kidney medicine · 2026Article
- Elucidation of a Novel Dual Binding Site on Tubulin: Theoretical Insights and Prospective Hybrid Inhibitors.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Precision spatiotemporal analysis of large-scale compound-protein interactions through molecular dynamics simulation.PNAS nexus · 2025Article
- Unveiling the Mechanisms of EGCG-p53 Interactions through Molecular Dynamics Simulations.ACS omega · 2024Article
- Article
- Systems engineering of Escherichia coli for high-level glutarate production from glucose.Nature communications · 2024Article
- Molecular Dynamics as a Tool for Virtual Ligand Screening.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.Journal of chemical information and modeling · 2023Article
- Crosslinking Rapidly Cured Epoxy Resin Thermosets: Experimental and Computational Modeling and Simulation Study.Polymers · 2023Article
- Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking.Biophysical reviews · 2022Review
- Ligand-induced shifts in conformational ensembles that describe transcriptional activation.eLife · 2022Article
- On the force field optimisation ofJournal of computer-aided molecular design · 2022Article
- In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses.Journal of medicinal chemistry · 2022Article
- From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output.Frontiers in pharmacology · 2022Review
- Probing the Suitability of Different CaMolecules (Basel, Switzerland) · 2021Article
- Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments.RSC advances · 2021Review
- Recent Developments in Positron Emission Tomography Tracers for Proteinopathies Imaging in Dementia.Frontiers in aging neuroscience · 2021Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Capturing the dynamic processes of biomolecular systems in atomistic detail remains difficult despite recent experimental advances. Although molecular dynamics (MD) techniques enable atomic-level observations, simulations of "slow" biomolecular processes (with timescales longer than submilliseconds) are challenging because of current computer speed limitations. Therefore, we developed a method to accelerate MD simulations by high-frequency ultrasound perturbation. The binding events between the protein CDK2 and its small-molecule inhibitors were nearly undetectable in 100-ns conventional MD, but the method successfully accelerated their slow binding rates by up to 10-20 times. Hypersound-accelerated MD simulations revealed a variety of microscopic kinetic features of the inhibitors on the protein surface, such as the existence of different binding pathways to the active site. Moreover, the simulations allowed the estimation of the corresponding kinetic parameters and exploring other druggable pockets. This method can thus provide deeper insight into the microscopic interactions controlling biomolecular processes.
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