Author

Zhe Wang

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Sep 2026

Predicting the Post-translational Modification Effects on Protein−Ligand Interactions via End-Point Binding Free Energy Calculation: Database Creation and Strategy Optimization

The experimentally validated PTM-mediated Ligand Activity Change (PLAC) dataset is curate and finds that the interaction-affecting PTMs usually occur spatially closer to ligands than the interaction-neutral ones.

Zi-Hao Wang, Xiao-Wei Xu, Zhe Wang et al. · Journal of Medicinal Chemist... · 0 citations

#natural language process... Jan 2026

How to efficiently characterize the interaction pathways of protein-ligand recognition? A comparative analysis on enhanced sampling approaches.

These results suggest that it will be much time-saving to utilize RAMD with high random force for interaction pathway exploration for both the pathway obvious and unobvious systems if the protein keeps stable in the simulation if the protein keeps stable in the simulation.

Zhiliang Jiang, Mingyun Shen, Zhe Wang et al. · Journal of Chemical Physics · 1 citation

#computer vision Jan 2026

Understanding the Kinetic Mechanism of Ligands Stabilizing the RAS-CYPA Interaction

This study leverages an integrated computational strategy combining molecular dynamics simulation, end-point binding free-energy calculation, and enhanced sampling technologies to elucidate the dynamic characteristics of RAS-ligand-CYPA interactions and uncover the dynamic process of stabilizer-mediated KRAS-CYPA stabi...

Kexin Xu, Mingyun Shen, Zhe Wang et al. · Journal of Chemical Informat... · 0 citations