EvoZymePro-Cat: A Protein–Ligand-Aware Deep Learning Framework for Predicting Mutation Effects in Enzyme Function

Enzymes are biological catalysts that speed up chemical reactions in an eco-friendly way. Precise enzyme design is hindered by vast sequence space and intricate sequence-structure-function interdependencies. To address these challenges, we developed EvoZymePro-Cat (EZPro-Cat), a deep learning platform for enzyme mutant screening. Conventional methods for predicting absolute mutant activities suffer from systematic errors and limited generalizability. Our pairwise comparison framework directly models relative activity superiority between variants, eliminating dependence on absolute value predictions. The framework integrates full sequence and local structure semantics of protein and ligand information using bilinear attention mechanisms. Protein sequences are encoded using the ESM1b transformer model. Ligands are represented through MolT5 embeddings and MACCS molecular fingerprints. The adaptability of protein residues to their microenvironments is captured by integrating structural features and site-specific evolutionary characteristics. Bilinear attention mechanisms capture long-range intermolecular interactions during catalysis by bidirectional projection and weighted fusion of protein-ligand features. Compared to existing methods, our model exhibits superior performance in identifying improved enzyme mutants through comparative prediction of mutation effects on activity, such as <i>K</i>_m and <i>k</i>_cat. For deep mutation scanning data sets, a few-shot learning strategy combined with the EZPro-Cat framework boosts prediction precision (AUC 0.908). By using integrated multimodal representations, EZPro-Cat offers a mechanistic and practical solution for functional profiling of intraprotein variants, driving paradigm shifts in highly efficient enzyme discovery and directed evolution.