Protein interactions are crucial for biological functions, yet pinpointing specificity-determining sites remains challenging. Here, the authors integrate local energetic frustration analysis with deep learning-based sequence generation method ProteinMPNN to identify these sites using two-component signaling systems, revealing how mutations regulate specificity and offering a strategy with broad implications for understanding protein evolution and interaction specificity.
- Yuqing Li
- Peng Li
- Zhiqiang Yan