Molecular dynamics (MD) is a powerful computational tool used for rational drug design in medicinal chemistry. MD is an extension of Molecular Mechanics, where the dynamic behavior of a molecular system is simulated through numerical integration of the equations of motion. This approach has been extensively used to aid and complement the design of novel ligands to a therapeutic target as well as to estimate their potency. Our review focuses on the basic theory of classical MD and their important applications in rational drug design of potential bioactive compounds, particularly anti-HIV compounds.
molecular dynamics; force field; drug design; anti-HIV activity
