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Author

Kai-Mo Yang

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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. · 0 citations
#computer vision May 2025

A Unified Deep Graph Model for Identifying the Molecular Categories of Ligands Targeting Nuclear Receptors

This study established a unified model (NRIGN) based on the deep graphic architecture to discriminate agonists and antagonists targeting 26 successful or in-clinical-trial NR targets and achieves an excellent prediction accuracy and is robust enough to be applied in various real-world scenarios.

Kaimo Yang, Dejun Jiang, Qirui Deng et al. · 2 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. · 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. · 0 citations

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