The search for new compounds with a given biological activity requires enormous effort in terms of manpower and cost. This effort arises from the large number of compounds that need to be synthesized and subsequently biologically evaluated. For this reason the pharmaceutical industry has shown great interest in theoretical methods that enable the rational design of pharmaceutical agents. In the last years bioinformatics has experienced a great evolution due to the development of specialized software and to the increasing computer power. The codification of the structural information of molecules through molecular descriptors and the subsequent data analysis allow establishing QSAR models (Quantitative Structure-Activity Relationship) that can be applied to the design and the virtual screening of new drugs. The development of sophisticated Docking methodologies also allows a more accurate predict of the biological activity of molecules. Moreover, through this type of computational techniques and theoretical approaches, it is possible to develop explanatory hypothesis on the mechanism of action of drugs. This work provides a brief description of a series of studies implemented in the software MOE (Molecular Operating Environment) with particular attention to the medicinal chemistry aspects.