3 papers
physics.comp-ph2026
Development and large-scale benchmarks of a protein--ligand absolute binding free energy toolkit
Yu Liu, Ailun Wang, Yu Xia +2
Absolute binding free energy (ABFE) calculations offer a theoretically rigorous approach for predicting protein--ligand binding affinities without the scaffold constraints of relat…
cs.LG2025
Generative molecule evolution using 3D pharmacophore for efficient Structure-Based Drug Design
Yi He, Ailun Wang, Zhi Wang +3
Recent advances in generative models, particularly diffusion and auto-regressive models, have revolutionized fields like computer vision and natural language processing. However, t…
cs.LG2024
Data-Driven Parametrization of Molecular Mechanics Force Fields for Expansive Chemical Space Coverage
Tianze Zheng, Ailun Wang, Xu Han +9
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanic…