Protein Language Pragmatic Analysis and Progressive Transfer Learning for Profiling Peptide–Protein Interactions

Protein complex structural data are growing at an unprecedented pace, but its complexity and diversity pose significant challenges for protein function research. Although deep learning models have been widely used to capture the syntactic structure, word semantics, or semantic meanings of polypeptide and protein sequences, these models often overlook the complex contextual information of sequences. Here, we propose interpretable interaction deep learning (IIDL)-peptide-protein interaction (PepPI), a deep learning model designed to tackle these challenges using data-driven and interpretable pragmatic analysis to profile PepPIs. IIDL-PepPI constructs bidirectional attention modules to represent the contextual information of peptides and proteins, enabling pragmatic analysis. It then adopts a progressive transfer learning framework to simultaneously predict PepPIs and identify binding residues for specific interactions, providing a solution for multilevel in-depth profiling. We validate the performance and robustness of IIDL-PepPI in accurately predicting peptide-protein binary interactions and identifying binding residues compared with the state-of-the-art methods. We further demonstrate the capability of IIDL-PepPI in peptide virtual drug screening and binding affinity assessment, which is expected to advance artificial intelligence-based peptide drug discovery and protein function elucidation.