ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery

The prediction of binary protein-protein interactions (PPIs) is essential for protein engineering, but a major challenge in deep learning-based methods is the unknown decision-making process of the model. To address this challenge, we propose the ESM2_AMP framework, which utilizes the ESM2 protein language model for extracting segment features from actual amino acid sequences and integrates the Transformer model for feature fusion in binary PPIs prediction. Further, the two distinct models, ESM2_AMPS and ESM2_AMP_CSE are developed to systematically explore the contributions of segment features and combine with special tokens features in the decision-making process. The experimental results reveal that the model relying on segment features demonstrates strong correlations between segments with high attention weights and known functional regions of amino acid sequences. This insight suggests that attention to these segments helps capture biologically relevant functional and interaction-related information. By analyzing the coverage relationship between high-attention sequence fragments and functional regions, we validated the model's ability to capture key segment features of PPIs and revealed the critical role of functional domains in PPIs. This finding not only enhances the interpretability methods for sequence-based prediction models but also provides biological evidence supporting the important regulatory role of functional sequences in protein-protein interactions. It offers cross-disciplinary insights for algorithm optimization and experimental validation research in the field of computational biology.