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Wengong Jin

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#artificial intelligence Preprint Sep 2026

Where Should Physics Enter a Molecular Crystal Generator?

Generative models make molecular crystal structure prediction fast, but their samples still exhibit geometric and packing violations. Physics can be introduced during training, post-training, or inference, yet these choices are rarely compared with the generator and physical signal held fixed. We introduce CrystAF, an...

Hao-Cheng Tang, Jun-Mei Wang, Wen-Gong Jin · 0 citations
#artificial intelligence Preprint Sep 2026

From Surfaces to Volumes: Registered Geometry for Protein Representation Learning

Existing protein geometry models typically represent molecular surfaces using local geometric features such as sampled points, normals, and curvature. While effective for capturing exposed molecular shape, these representations do not explicitly model the volumetric organization beneath the surface or provide a consist...

Si-Yuan Chen, Cai Zhou, Jin-Rui Zhang et al. · 0 citations
Open access Aug 2026

Elucidating enzyme–substrate specificity through co-folding foundation model

Boltz2ESI is introduced, an end-to-end framework that predicts enzyme–substrate interactions by leveraging structural knowledge learned by a biomolecular foundation model and consistently outperforms state-of-the-art sequence-based and rigid-docking approaches.

Xi-Wei Cheng, Seonghwan Seo, C. Huh et al. · 0 citations

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