With the rapid advancements in computer technology and bioinformatics, the prediction of protein-ligand binding sites has become a central component of modern drug discovery and development. Traditional experimental methods are often constrained by long experimental cycles and high costs; therefore, the development of accurate and efficient computational methods is of paramount significance for conserving time and cost. This review comprehensively summarizes the methodological advancements and current applications in the field of screening for druggable protein target sites, systematically comparing the fundamental principles, advantages, and disadvantages of four main categories of methods: structure- and sequence-based methods, machine learning-based methods, binding site feature analysis methods, and druggability assessment methods. Subsequently, by integrating classic case studies, this paper elaborately discusses the technical support and theoretical guidance afforded by the screening of protein druggable target sites for drug discovery and drug repositioning. Finally, this paper thoroughly explores the current challenges inherent in the field of protein-ligand binding site prediction, with a particular focus on future technological trends, systematically elucidating the developmental prospects and potential applications of these predictive methods.