Author

Ziyi You

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Open access Sep 2026

RFOptimization: Guiding Design Optimization with All-Atom Structure Prediction

RFO formulates binder improvement as a residue-wise mutational search problem, sampling candidate substitutions alternately based on gradient-guided sequence optimization using all-atom structure prediction models and a cycling-based sequence redesign strategy that alternates structure generation with an orthogonal pre...

Odin Zhang, Jia-Qi Wang, T. R. Thompson et al. · bioRxiv · 0 citations

#computer vision Open access Jul 2025

A scalable and quantum-accurate foundation model for biomolecular force fields via linearly tensorized quadrangle attention

LiTEN achieves state-of-the-art accuracy on standard benchmarks, consistently outperforming leading approaches in both precision and speed, and enables comprehensive modeling tasks, ranging from geometry optimization to free energy surface construction, with high computational efficiency for large biomolecules.

Qun Su, Kai Zhu, Qiaolin Gou et al. · Nature Communications · 2 citations

Open access Aug 2026

NACraft: Programmatic nucleic-acid aptamer design via all-atom structure-model feedback

NACraft, a training-free and programmatic framework for all-atom nucleic-acid aptamer design based on backpropagation through structure-model feedback, is presented, demonstrating the effectiveness and versatility of NACraft and extending structure-model hallucination toward programmatic nucleic-acid aptamer design.

He-Qin Zhu, Jiaqi Wang, Wei-Bo Zhao et al. · bioRxiv · 0 citations