Modeling and visualization of protein–ligand interactions has played a key role in the design of a number of marketed drugs for the treatment of several diseases. In this work we review the original papers reported in the literature pointing out the contribution of the so–called structure–based drug design to the drug development process. We propose the use of molecular viewers as valuable tools to interact with the three dimensional structures, obtained through the Protein Data Bank, and to better understand the drug design strategy. An introduction to common computational techniques employed in structure–based drug design, such as automated molecular docking, and web-based computational approaches to convert protein sequences into 3D-models, are also provided. The case studies and Internet resources reviewed in this work can be included in drug design topics covered in organic and medicinal chemistry courses.