ArticleJournal of chemical theory and computation2021
Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Enhancing Relative Binding Free Energy Calculation with Grand Canonical Monte Carlo, Water-swap Monte Carlo, Terminal-flip Monte Carlo and Replica Exchange Solute Tempering.Journal of chemical theory and computation · 2026Article
- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.Journal of chemical information and modeling · 2026Article
- A Quadrupolar Fullerene Model System for Benchmarking Enhanced Sampling of Trapped Waters in Free Energy Calculations.The journal of physical chemistry. B · 2026Article
- Combining an OSMAC approach and untargeted metabolomics to profile compounds exhibiting anti-HIV-1 activities in an endophytic fungus, Penicillium Rubens P03MB2.Scientific reports · 2025Article
- Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations.Journal of chemical information and modeling · 2025Article
- Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields.Journal of chemical theory and computation · 2024Article
- Accelerated Enveloping Distribution Sampling to Probe the Presence of Water Molecules.Journal of chemical theory and computation · 2023Article
- WaterKit: Thermodynamic Profiling of Protein Hydration Sites.Journal of chemical theory and computation · 2023Article
- Unveiling the Inhibitory Potentials of Peptidomimetic Azanitriles and Pyridyl Esters towards SARS-CoV-2 Main Protease: A Molecular Modelling Investigation.Molecules (Basel, Switzerland) · 2023Article
- Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo.Journal of chemical theory and computation · 2023Article
- Proteome-Wide Screening of Potential Vaccine Targets againstVaccines · 2023Article
- Unraveling Complex Local Protein Environments with 4-Cyano-l-phenylalanine.The journal of physical chemistry. B · 2022Article
- Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization.Life (Basel, Switzerland) · 2022Review
- Absolute binding free energy calculations improve enrichment of actives in virtual compound screening.Scientific reports · 2022Article
- In Silico Drug Repurposing of FDA-Approved Drugs Highlighting Promacta as a Potential Inhibitor of H7N9 Influenza Virus.Molecules (Basel, Switzerland) · 2022Article
- Structural Investigations and Binding Mechanisms of Oseltamivir Drug Resistance Conferred by the E119V Mutation in Influenza H7N9 Virus.Molecules (Basel, Switzerland) · 2022Article
- Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants.Journal of the American Chemical Society · 2022Article
- Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques.Journal of chemical theory and computation · 2022Article
- Intermolecular Mechanism and Dynamic Investigation of Avian Influenza H7N9 Virus' Susceptibility to E119V-Substituted Peramivir-Neuraminidase Complex.Molecules (Basel, Switzerland) · 2022Article
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Authors and funding
5 authors.
Funding
Abstract
Molecular dynamics (MD) simulations of proteins are commonly used to sample from the Boltzmann distribution of conformational states, with wide-ranging applications spanning chemistry, biophysics, and drug discovery. However, MD can be inefficient at equilibrating water occupancy for buried cavities in proteins that are inaccessible to the surrounding solvent. Indeed, the time needed for water molecules to equilibrate between the bulk solvent and the binding site can be well beyond what is practical with standard MD, which typically ranges from hundreds of nanoseconds to a few microseconds. We recently introduced a hybrid Monte Carlo/MD (MC/MD) method, which speeds up the equilibration of water between buried cavities and the surrounding solvent, while sampling from the thermodynamically correct distribution of states. While the initial implementation of the MC functionality led to considerable slowing of the overall simulations, here we address this problem with a parallel MC algorithm implemented on graphical processing units. This results in speed-ups of 10-fold to 1000-fold over the original MC/MD algorithm, depending on the system and simulation parameters. The present method is available for use in the AMBER simulation software.
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