arXiv Machine Learning August 18, 2026 By Yang Zhang, Zhewei Wei, Ye Yuan, Chongxuan Li, Wenbing Huang

EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction

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EquiPocket is an E(3)-equivariant Graph Neural Network designed to predict ligand binding sites on proteins. It processes proteins as geometric graphs, extracting local surface atom geometry, modeling chemical and spatial relationships, and performing equivariant message passing to capture surface geometry. A dense attention output layer mitigates issues caused by variable protein sizes, and experiments show the method outperforms current state‑of‑the‑art approaches.

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