Computer-aided drug discovery (CADD) has revolutionized the field of
pharmaceutical research by providing efficient tools for predicting and optimizing
drug-target interactions. Molecular dynamics (MD) simulations, an essential technique
within CADD, play a crucial role in understanding the dynamic behavior of
biomolecules and their interactions with potential drug candidates. In this chapter, we
explore the principles, methodologies, applications, and advancements of MD
simulations in the context of drug discovery. It highlights how MD simulations can
provide detailed insights into biomolecular systems' structural dynamics, energetics,
and kinetics, facilitating the rational design of novel therapeutics. By shedding light on
the remarkable potential of MD simulations, we aim to underscore their significance in
accelerating the drug discovery process and driving the development of targeted drugs.
Keywords: Biomolecular interactions, Boundary conditions, Computer-aided drug discovery, Force field, Molecular dynamics, Newton’s equation, Simulation box.
