Significant progress over the past decade in virtual representations of molecules and their physicochemical properties has produced new drugs from virtual screening of the structures of single protein molecules by conventional modeling methods. The development of clinical antiviral drugs from structural data for HIV protease has been a major success in structure based drug design. Techniques for virtual screening involve the ranking of the affinity of potential ligands for the target site on a protein. Two main alternatives have been developed: modeling of the target protein with a series of related ligand molecules, and docking molecules from a database to the target protein site. The computational speed and prediction accuracy will depend on the representation of the molecular structure and chemistry, the search or simulation algorithm, and the scoring function to rank the ligands. Moreover, the general challenges in modern computational drug design arise from the profusion of data, including whole genomes of DNA, protein structures, chemical libraries, affinity and pharmacological data. Therefore, software tools are being developed to manage and integrate diverse data, and extract and visualize meaningful relationships. Current areas of research include the development of searchable chemical databases, which requires new algorithms to represent molecules and search for structurally or chemically similar molecules, and the incorporation of machine learning techniques for data mining to improve the accuracy of predictions. Examples will be presented for the virtual screening of drugs that target HIV protease.