InterPreTS (Interaction Prediction through Tertiary Structure) is a web-based version of our method for predicting protein-protein interactions (Aloy and Russell, 2002, PROC: Natl Acad. Sci. USA, 99, 5896-5901). Given a pair of query sequences, we first search for homologues in a database of interacting domains (DBID) of known three-dimensional complex structures. Pairs of sequences homologous to a known interacting pair are scored for how well they preserve the atomic contacts at the interaction interface. InterPreTS includes a useful interface for visualising molecular details of any predicted interaction.