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NEAT-POCKET: Pocket-Conditioned Autoregressive 3D Molecular Generation with a Neighborhood-Guided Set Transformer

arXiv · AI, language, vision and robotics · article · Sep 4, 2026 · UTC

AI-driven de novo molecular design offers a promising route to accelerate early-stage drug discovery by generating novel ligands directly within target protein binding pockets. We present NEAT-POCKET, a pocket-conditioned extension of the autoregressive NEAT model for 3D molecular generation. NEAT-POCKET generates molecules atom by atom in protein pocket environments while preserving atom permutation invariance and explicitly modeling hydrogen atoms. Benchmarks on the CrossDocked and SPINDR datasets show that NEAT-POCKET achieves competitive structure-based generation performance while samplin

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