This review provides an in-depth analysis of protein–ligand interactions, focusing on the physicochemical mechanisms, binding models, and experimental/theoretical methods used to study these interactions. Protein–ligand binding is a fundamental process in biological systems, enabling molecular recognition and function. Understanding the mechanisms behind these interactions is crucial for drug discovery and development, as it allows for the rational design of drugs that target specific protein–ligand interactions. The review begins by discussing the physicochemical mechanisms underlying protein–ligand binding, including binding kinetics, thermodynamic concepts, and the driving forces that govern the interaction. It then introduces three key models for protein–ligand binding: the "lock-and-key" model, which assumes rigid protein and ligand interfaces; the "induced fit" model, which accounts for conformational changes in the protein upon ligand binding; and the "conformational selection" model, which suggests that the protein adopts a conformation that is compatible with the ligand before binding occurs. Each model is discussed in terms of its thermodynamic basis and how it explains the binding process. The review also covers the experimental and computational methods used to investigate protein–ligand binding affinity. Experimental methods include isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), and fluorescence polarization (FP), which provide insights into the thermodynamics and kinetics of binding. Computational methods, such as protein–ligand docking and free energy calculations, are also discussed, highlighting their roles in predicting binding modes and affinities. The review concludes by emphasizing the importance of understanding the thermodynamic and enthalpic contributions to protein–ligand binding, as well as the role of entropy in determining binding affinity. It also discusses the challenges and limitations of current methods, and highlights the need for a comprehensive understanding of these interactions to advance drug discovery and molecular biology.This review provides an in-depth analysis of protein–ligand interactions, focusing on the physicochemical mechanisms, binding models, and experimental/theoretical methods used to study these interactions. Protein–ligand binding is a fundamental process in biological systems, enabling molecular recognition and function. Understanding the mechanisms behind these interactions is crucial for drug discovery and development, as it allows for the rational design of drugs that target specific protein–ligand interactions. The review begins by discussing the physicochemical mechanisms underlying protein–ligand binding, including binding kinetics, thermodynamic concepts, and the driving forces that govern the interaction. It then introduces three key models for protein–ligand binding: the "lock-and-key" model, which assumes rigid protein and ligand interfaces; the "induced fit" model, which accounts for conformational changes in the protein upon ligand binding; and the "conformational selection" model, which suggests that the protein adopts a conformation that is compatible with the ligand before binding occurs. Each model is discussed in terms of its thermodynamic basis and how it explains the binding process. The review also covers the experimental and computational methods used to investigate protein–ligand binding affinity. Experimental methods include isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), and fluorescence polarization (FP), which provide insights into the thermodynamics and kinetics of binding. Computational methods, such as protein–ligand docking and free energy calculations, are also discussed, highlighting their roles in predicting binding modes and affinities. The review concludes by emphasizing the importance of understanding the thermodynamic and enthalpic contributions to protein–ligand binding, as well as the role of entropy in determining binding affinity. It also discusses the challenges and limitations of current methods, and highlights the need for a comprehensive understanding of these interactions to advance drug discovery and molecular biology.