Molecular docking is a computational technique utilized in the field of structural biology and drug discovery. It aims to predict the binding orientation and affinity between two or more molecules, typically a protein and a ligand (small molecule), by simulating their interaction within a defined three-dimensional space. The process involves generating multiple conformations of the ligand and exploring various binding poses within the binding site of the protein. By evaluating intermolecular interactions, such as hydrogen bonds, hydrophobic interactions, and electrostatic forces, docking algorithms estimate the binding energy and thereby predict the strength of the binding interaction. Molecular docking plays a critical role in understanding molecular recognition, deciphering protein-ligand interactions, and aiding in the discovery of potential drug candidates. The technique has wide-ranging applications, including virtual screening of compound libraries, lead optimization, and elucidating the mechanisms of molecular interactions. Through the integration of computational simulations and structural biology data, molecular docking contributes to the acceleration of drug discovery processes and the exploration of molecular interactions that underlie pyrimidine derivatives' significance spans their roles in fundamental cellular processes, such as DNA and RNA synthesis, as well as their utility in drug discovery and development. These derivatives have been extensively studied for their interactions with enzymes, receptors, and other biomolecules, making them crucial components in fields like medicinal chemistry and molecular biology. In drug discovery, pyrimidine derivatives have been exploited as scaffolds for designing drugs targeting a variety of diseases, including cancer, viral infections, inflammation, and metabolic disorders. Their versatile nature allows for structural modifications to enhance binding affinities, selectivity, and pharmacokinetic properties, resulting in compounds with improved therapeutic profiles. Furthermore, pyrimidine derivatives have contributed to advancements in personalized medicine, as specific modifications can be tailored to individual genetic variations or disease conditions. The elucidation of their molecular interactions through computational simulations and structural studies has enabled the rational design of novel drug candidates and the optimization of existing ones.various biological phenomena.