Yoon, Min Su Bae, Byunghyun Kim, Kunhee Park, Hahnbeom Baek, Minkyung 2025-03-20T15:30:14Z 2025-03-20T15:30:14Z 2025-03-19 2025-02 0959-440X https://pubs.kist.re.kr/handle/201004/151933 Proteome-scale interaction prediction is essential for understanding protein functions and disease mechanisms. Traditional experimental methods are often limited by scale and complexity, driving the need for computational approaches. Deep learning has emerged as a powerful tool, enabling highthroughput, accurate predictions of protein interactions. This review highlights recent advances in deep learning methods for protein-protein and protein-ligand interaction screening, along with datasets used for model training. Despite the progress with deep learning, challenges such as data quality and validation biases remain. We also discuss the increasing importance of integrating structural information to enhance prediction accuracy and how structure-based deep learning approaches can help overcome current limitations, ultimately advancing biological research and drug discovery. English Elsevier BV Deep learning methods for proteome-scale interaction prediction Article 10.1016/j.sbi.2024.102981 1 Current Opinion in Structural Biology, v.90 Current Opinion in Structural Biology 90 N scie scopus 001408107700001 2-s2.0-85215372782 Biochemistry & Molecular Biology Cell Biology Biochemistry & Molecular Biology Cell Biology Article SMALL-MOLECULE TARGETS