ArticleJournal of chemical theory and computation2019
Simulating Water Exchange to Buried Binding Sites.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 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
- A Quadrupolar Fullerene Model System for Benchmarking Enhanced Sampling of Trapped Waters in Free Energy Calculations.The journal of physical chemistry. B · 2026Article
- Toward Reconciling the Standard Binding Free Energy of Lenacapavir to HIV-1 Capsid with Experiment: Thermodynamic Effects of Solvent Buffer and Ligand Reorganization.The journal of physical chemistry. B · 2026Article
- Accurate predictions of protein mutational effects accelerated with a hybrid-topology free energy protocol.Communications chemistry · 2025Article
- Assignment of a Physical Energy Scale for the Dimensionless Interaction Energies within the PRIME20 Peptide Model.Chemphyschem : a European journal of chemical physics and physical chemistry · 2024Article
- Investigating the Regulation of Ribosomal Protein S6 Kinase 1 by CoAlation.International journal of molecular sciences · 2024Article
- Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2023Article
- WaterKit: Thermodynamic Profiling of Protein Hydration Sites.Journal of chemical theory and computation · 2023Article
- Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities.Journal of chemical information and modeling · 2023Article
- Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo.Journal of chemical theory and computation · 2023Article
- Water Networks in Complexes between Proteins and FDA-Approved Drugs.Journal of chemical information and modeling · 2023Article
- Functional Water Networks in Fully Hydrated Photosystem II.Journal of the American Chemical Society · 2022Article
- Evaluating the use of absolute binding free energy in the fragment optimisation process.Communications chemistry · 2022Article
- py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD.Journal of chemical theory and computation · 2022Article
- Spatially Resolved Hydration Thermodynamics in Biomolecular Systems.The journal of physical chemistry. B · 2022Review
- Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks.ACS physical chemistry Au · 2022Article
- Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.Nature protocols · 2022Review
- Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units.Journal of chemical theory and computation · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Traditional molecular dynamics (MD) simulations of proteins, which relies on integration of Newton's equations of motion, cannot efficiently equilibrate water occupancy for buried cavities in proteins. This leads to slow convergence of thermodynamic averages for such systems. We have addressed this challenge by efficiently integrating standard Metropolis Monte Carlo (MC) translational water moves with MD in the AMBER simulation package. The translational moves allow water to easily enter or exit buried sites in a thermodynamically correct way during a simulation. To maximize efficiency, the algorithm avoids moves that only interchange waters within the bulk around the protein instead focusing on moves that can transfer water between bulk and the protein interior. In addition, a steric grid allows avoidance of moves that would lead to obvious steric clashes, and a fast grid-based energy evaluation is used to reduce the number of expensive full energy calculations. The potential energy distribution produced using MC/MD was found to be statistically indistinguishable from that of control simulations using only MD, and the algorithm effectively equilibrated water across steric barriers and into binding pockets that are not accessible with pure MD. The MC/MD method introduced here should be of increasing utility for applications spanning protein folding, the elucidation of protein mechanisms, and free energy calculations for computer-aided drug design. It is available in version 18 release of the widely disseminated AMBER simulation package.
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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.