Protein-peptide Interaction Representation Learning with Pretrained Language Models

Abstract

Protein-peptide Interactions (PpIs) paly essential roles in diverse cellular processes, yet their systematic identification remains challenging due to the limited availability of experimentally annotated protein-peptide interaction data. To address this challenge, we present PepInter, a sequence-based Deep Learning (DL) framework that leverages large-scale pretraining on structurally derived pseudo protein-peptide pairs to learn interaction-relevant representations. Specifically, energy-dominant peptide fragments are extracted from protein complexes curated from non-redundant Protein Data Bank (PDB) structures, enabling the construction of pseudo protein-peptide interaction pairs that capture interface interaction patterns shared with canonical protein-protein interactions. This strategy allows the model to acquire interaction-aware priors in the absence of large-scale annotated protein-peptide complex datasets. Built upon the ESM-Cambrian (ESMC) architecture, PepInter adopts a two-stage pretraining strategy. In the first stage, masked language modeling is used to learn general protein sequence representations. In the second stage, the model is further trained to predict Rosetta-derived energetic scores, explicitly incorporating structural interaction signals into the learned embeddings. Following pretraining, PepInter is fine-tuned for both protein-peptide interaction classification and peptide bioactivity regression tasks. Across multiple benchmark datasets, including protein-peptide binding affinity prediction, PepInter consistently outperforms existing baseline methods and demonstrates strong generalization in identifying biologically meaningful PpIs. Case studies further highlight its ability to recover known interaction patterns and predict novel protein-peptide interactions. Together, these results establish PepInter as a scalable and effective framework for protein-peptide interaction prediction, with strong potential to accelerate peptide-based drug discovery.