Discovery of a similar region on two protein surfaces can lead to important inference about the functional role or molecular interaction of this region for one of the proteins if such information is available for the other. This tutorial will present the basic principles of protein-protein interactions and review recent approaches to compare protein surfaces and to recognize binding sites. It will focus on the geometric aspects of the protein surface comparison problem. Topics covered include local shape descriptors for the representations of the surfaces; basic data structures for modelling proteins; similarity measures; motif finding for the functional annotation of proteins; application of methods developed in the area of computer vision to problems in protein structure comparison.