Advances in, and dissemination of, computer technologies in the field of drug research now enable the use of molecular modeling tools to teach important concepts of drug design to chemistry and pharmacy students. A series of computer laboratories is described to introduce undergraduate students to commonly adopted "in silico" drug design methods, such as molecular geometry optimization, pharmacophore modeling, protein-ligand docking simulations, homology modeling, virtual screening, and pharmacokinetics/toxicity predictions. Freely available software and web servers are selected to compose this pedagogical resource, such that it can be easily implemented in any institution equipped with an Internet connection and Windows OS computers. This material is an illustration of a drug discovery pipeline, starting from the structure of known drugs to obtain novel bioactive compounds, and, therefore, is a valid pedagogical instrument for educating future professionals in the field of drug development.