Drug-target interaction/affinity prediction: Deep learning models and advances review

Drug discovery remains a slow and expensive process that involves many steps, from detecting the target structure to obtaining approval from the Food and Drug Administration (FDA), and is often riddled with safety concerns. Accurate prediction of how drugs interact with their targets and the development of new drugs by using better methods and technologies have immense potential to speed up this process, ultimately leading to faster delivery of life-saving medications. Traditional methods used for drug-target interaction and affinity prediction show limitations, particularly in capturing complex relationships between drugs and their targets. As an outcome, deep learning models have been presented to overcome the challenges of interaction prediction through their precise and efficient end results. By outlining promising research avenues and models, each with a different solution but similar to the problem, this paper aims to give researchers a better idea of methods for even more accurate and efficient prediction of drug-target interaction/affinity, ultimately accelerating the development of more effective drugs. A total of 180 methods for drug-target interaction/affinity prediction were analyzed throughout the period spanning 2016 to 2025 using different frameworks based on machine learning, mainly deep learning and graph neural networks. Additionally, this paper discusses the novelty, architecture, and input representation of these models.