The rapid increase in the number of high-quality protein structures provides an expanding knowledge resource about interactions involved in stabilizing protein three-dimensional structures and the complexes they form with other molecules. In this paper we first review the results of some recent analyses of protein structure, including restrictions on local conformation, and a study of the geometry of hydrogen bonds. Then we consider how such empirical data can be used as a test bed for energy calculations, by using the observed spatial distributions of side chain/atom interactions to assess three different methods for modelling atomic interactions in proteins. We have also derived a new empirical solvation potential which aims to reproduce the hydrophobic effect. To conclude we address the problem of molecular recognition and consider what we can deduce about the interactions involved in the binding of peptides to proteins.