Structure-aware Reinforcement Learning for Protein Directed Evolution

Zikun Nie, Suyuan Zhao, Yizhen Luo, Siqi Fan, Zaiqing Nie

Protein optimization remains a longstanding goal in life sciences. Existing machine learning-assisted directed evolution (MLDE) methods primarily rely on sequence-only features, overlooking the critical spatial constraints and co-evolutionary interactions encoded in protein structures. However, directly integrating structural information remains challenging due to the scarcity of reliable mutant structures. To address these issues, we propose StructEvo, a novel structure-aware reinforcement learning framework for protein directed evolution. StructEvo employs a delta-structure fusion encoder to approximate mutant structure features via feature differences, enabling dynamic incorporation of spatial knowledge. The vast mutation space is then decomposed into manageable subspaces through a structure-aligned hierarchical action network, while a geometric constraint further stabilizes delta feature learning. Our approach outperforms prior state-of-the-art methods by 9.2% and 16.3% on two challenging optimization benchmarks, and further identifies an experimentally validated epistasis pattern in GFP, highlighting the importance of structural guidance for effective protein directed…