ABSTRACT
Structural genomics programs around the world are delivering an abundance of threedimensional (3-D) structures of proteins, some of which are pharmacologically highly relevant. Hence, computer programs for automatic docking of libraries of compounds are being developed further and applied to design drugs against a plethora of diseases including AIDS, Alzheimer’s disease, cancer, malaria, and sleeping sickness. In this chapter, we first review the most common approaches for structure-based flexible ligand docking. Some technical improvements for more efficient sampling and more appropriate scoring functions are then presented. Finally, a number of practical suggestions are given for high throughput docking (HTD) with special emphasis on our fragment-based approach.
