Pharmaceutical Chemistry at the ETH Zürich is devoted to research on structure–activity relationships. The combination of biophysical methods, like protein crystallography, mass spectrometry and NMR, with theoretical approaches such as QSAR studies and molecular mechanical as well as quantum mechanical molecular modeling yield insight into ligand–protein recognition and has enabled a more fundamental understanding of ligand binding and transformation in several classes of proteins. The main biological targets are and have been, kinases, major histocompatibility proteins, peptide hormones and most recently glycoproteins. In parallel the results fostered the improvement and new development of appropriate software tools for molecular design studies, the most recent of which is the automated integration of tautomeric states in docking.