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EnerBridge-DPO: Energy-Guided Protein Inverse Folding with Markov Bridges and Direct Preference Optimization
Dingyi Rong, Haotian Lu, Wenzhuo Zheng, Fan Zhang, Shuangjia Zheng, Ning Liu
https://arxiv.org/abs/2506.09496

EnerBridge-DPO: Energy-Guided Protein Inverse Folding with Markov Bridges and Direct Preference Optimization
Designing protein sequences with optimal energetic stability is a key challenge in protein inverse folding, as current deep learning methods are primarily trained by maximizing sequence recovery rates, often neglecting the energy of the generated sequences. This work aims to overcome this limitation by developing a model that directly generates low-energy, stable protein sequences. We propose EnerBridge-DPO, a novel inverse folding framework focused on generating low-energy, high-stability prot…