Structure-based drug design uses three-dimensional visualization of drug candidates bound to a target receptor to direct structural modifications that increase potency. This widely used approach is limited by the difficulty of accurately predicting drug-binding affinities from three-dimensional structures. The integration of structure-based drug design with combinatorial chemistry can overcome this limitation by providing an empirical understanding of drug-binding energies. This integration allows compound synthesis and evaluation in parallel, and also helps assure that the compounds produced have properties consistent with good bioavailability and safety.