Divide-and-Conquer ABFE: Improving Free Energy Calculations by Enhancing Water Sampling DOI
Runduo Liu,

Yufen Yao,

Wanyi Huang

et al.

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: March 24, 2025

Free energy perturbation (FEP) is a promising method for accurately predicting molecular interactions, widely applied in fields such as drug design, materials science, and catalysis. However, FEP calculations, particularly those aqueous environments, often suffer from convergence issues due to insufficient sampling of water molecules. These challenges are critical solvation-related free small molecule-protein binding, interface adsorption on surfaces. To address these limitations, we present the divide-and-conquer absolute binding (DC-ABFE) method. By partitioning ligand or molecule into atomic groups sequentially decoupling their van der Waals DC-ABFE improves re-entry sampling, enhances phase-space overlap, significantly calculations. Our benchmark demonstrates that achieves more reproducible reliable predictions compared traditional methods. applicable range calculations involving solvation effects. Additionally, this establishes stronger foundation precise screening, offering robust tool affinities discovery.

Language: Английский

Loading α-helical peptide drugs onto nanotubes: Influence of surface curvature and van der Waals/electrostatic interactions DOI
Qu Chen

Applied Surface Science, Journal Year: 2025, Volume and Issue: unknown, P. 162467 - 162467

Published: Jan. 1, 2025

Language: Английский

Citations

2
Divide-and-Conquer ABFE: Improving Free Energy Calculations by Enhancing Water Sampling DOI
Runduo Liu,

Yufen Yao,

Wanyi Huang

et al.

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: March 24, 2025

Free energy perturbation (FEP) is a promising method for accurately predicting molecular interactions, widely applied in fields such as drug design, materials science, and catalysis. However, FEP calculations, particularly those aqueous environments, often suffer from convergence issues due to insufficient sampling of water molecules. These challenges are critical solvation-related free small molecule-protein binding, interface adsorption on surfaces. To address these limitations, we present the divide-and-conquer absolute binding (DC-ABFE) method. By partitioning ligand or molecule into atomic groups sequentially decoupling their van der Waals DC-ABFE improves re-entry sampling, enhances phase-space overlap, significantly calculations. Our benchmark demonstrates that achieves more reproducible reliable predictions compared traditional methods. applicable range calculations involving solvation effects. Additionally, this establishes stronger foundation precise screening, offering robust tool affinities discovery.

Language: Английский

Citations

0