This review discusses the significant role of atomistic computer simulations, specifically molecular dynamics (MD) simulations, in drug discovery. These simulations can identify cryptic or allosteric binding sites, enhance traditional virtual-screening methodologies, and directly predict small-molecule binding energies. The limitations of current simulation methodologies, such as high computational costs and approximations of molecular forces, are also addressed. Despite these challenges, the future of computer-aided drug design is promising due to ongoing improvements in computer power and algorithm design. MD simulations are expected to play an increasingly important role in the development of novel pharmacological therapeutics.This review discusses the significant role of atomistic computer simulations, specifically molecular dynamics (MD) simulations, in drug discovery. These simulations can identify cryptic or allosteric binding sites, enhance traditional virtual-screening methodologies, and directly predict small-molecule binding energies. The limitations of current simulation methodologies, such as high computational costs and approximations of molecular forces, are also addressed. Despite these challenges, the future of computer-aided drug design is promising due to ongoing improvements in computer power and algorithm design. MD simulations are expected to play an increasingly important role in the development of novel pharmacological therapeutics.