In molecular docking simulations, evaluating the quality of contacts between ligands and receptors depends on scoring functions, so the molecular mechanism of docking mainly consists of their usage. By evaluating several elements, including intermolecular forces, steric conflicts, hydrogen bonding, and electrostatic interactions, scoring systems in docking algorithms evaluate and rank possible binding positions. Forecasting the binding affinity between a ligand and a receptor is one of these purposes; this is crucial for discovering potential drug candidates. Standard scoring systems are empirical, which uses pre-defined criteria, and physics-based, which uses computational models derived from basic physical principles. The dependability of docking predictions depends much on the precision of scoring systems, affecting structural biology and drug discovery research's decision-making. Maximising docking protocols and improving the accuracy and efficiency of molecular docking simulations depend on a knowledge of the complexity of scoring systems.