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The use of computer-aided drug design has been acknowledged as a potent tool in the drug discovery pipeline due to the high costs and length of time involved in bringing a commercial medicine to market. Over the past ten years, molecular modeling tools have seen a significant increase in computer power to speed up drug discovery. The cost and time needed for the discovery of a useful drug are now being reduced by pharmaceutical corporations and academic research organizations utilizing a variety of computational modeling methodologies. In this article, we will explore three important aspects of molecular modeling—Molecular Docking, Molecular Dynamics, and ADMET modeling—as well as their uses and restrictions in the development of small-molecule drugs. The technical aspects of molecular dynamics and docking, the algorithms used to create docking software, the models investigated by these algorithms, and their scoring functions were all covered in our discussion. We also discussed the role that molecular dynamics simulations—both coarse- and all-atom simulations—play in the process of finding new drugs.