Prediction of protein-protein interactions and co-complex models with deep learning

Protein-protein interactions (PPIs) are fundamental to cellular processes, and essential for understanding biological function and disease mechanisms. In this review, we emphasize recent deep learning-based methods for protein interaction study. Focusing on three closely related tasks of proteome-wide PPI prediction, PPI interface prediction, and PPI co-complex structure prediction, we discuss how emerging concepts and computation approaches have evolved to shape these fields We categorize recent approaches according to their methodological paradigms, summarize their strengths and limitations, and further explore diverse biological and biomedical applications, highlighting how computational methods in PPI prediction, PPI interface prediction, and PPI structure prediction jointly contribute to understanding of complex biological systems.