ArticleThe Journal of chemical physics2018
Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics.
Article in The Journal of chemical physics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Markovian state models uncover casein kinase 1 dynamics that govern circadian period.Biophysical journal · 2025Article
- Mechanisms of Peptide Agonist Dissociation and Deactivation of Adhesion G-Protein-Coupled Receptors.Biochemistry · 2025Article
- Mechanisms of peptide agonist dissociation and deactivation of adhesion G-protein-coupled receptors.bioRxiv : the preprint server for biology · 2024Article
- Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.Journal of chemical theory and computation · 2024Article
- Ligand Gaussian accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.bioRxiv : the preprint server for biology · 2024Article
- Mechanism of Ligand Binding to Theophylline RNA Aptamer.Journal of chemical information and modeling · 2024Article
- Study on the Mechanism of Interaction between Dipeptidyl Peptidase 4 and Inhibitory Peptides Based on Gaussian Accelerated Molecular Dynamic Simulation.International journal of molecular sciences · 2024Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- Nitazoxanide Inhibits the Bifunctional Enzyme GlG6PD::6PGL ofInternational journal of molecular sciences · 2023Article
- Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.Journal of chemical theory and computation · 2023Article
- Stomatal COScience advances · 2022Article
- Protein-Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics.Journal of chemical theory and computation · 2022Article
- Most Probable Druggable Pockets in Mutant p53-Arg175His Clusters Extracted from Gaussian Accelerated Molecular Dynamics Simulations.The protein journal · 2022Article
- Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective.Frontiers in molecular biosciences · 2022Review
- Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling.Journal of chemical theory and computation · 2021Article
- Mechanism of Ligand Recognition by Human ACE2 Receptor.The journal of physical chemistry letters · 2021Article
- Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations.STAR protocols · 2021Article
- Mechanism of ligand recognition by human ACE2 receptor.bioRxiv : the preprint server for biology · 2020Article
- Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding.The Journal of chemical physics · 2020Article
- Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics.Journal of chemical theory and computation · 2020Article
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Abstract
Recent studies demonstrated that Gaussian accelerated molecular dynamics (GaMD) is a robust computational technique, which provides simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. However, the exact acceleration of biomolecular dynamics or speedup of kinetic rates in GaMD simulations and, more broadly, in enhanced sampling methods, remains a challenging task to be determined. Here, the GaMD acceleration is examined using alanine dipeptide in explicit solvent as a biomolecular model system. Relative to long conventional molecular dynamics simulation, GaMD simulations exhibited ∼36-67 times speedup for sampling of the backbone dihedral transitions. The acceleration depended on level of the GaMD boost potential. Furthermore, Kramers' rate theory was applied to estimate GaMD acceleration using simulation-derived diffusion coefficients, curvatures and barriers of free energy profiles. In most cases, the calculations also showed significant speedup of dihedral transitions in GaMD, although the GaMD acceleration factors tended to be underestimated by ∼3-96 fold. Because greater boost potential can be applied in GaMD simulations of systems with increased sizes, which potentially leads to higher acceleration, it is subject to future studies on accelerating the dynamics and recovering kinetic rates of larger biomolecules such as proteins and protein-protein/nucleic acid complexes.
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