I will discuss some of the work my group has been doing on predicting protein interaction networks, and analyzing them to uncover protein functions and pathways. We have developed a general structural bioinformatics framework for predicting protein interactions that can be applied to specific structural motifs. Our framework incorporates both sequence and experimental data, and we will demonstrate its effectiveness in predicting certain types of protein-protein and protein-DNA interactions. I will also present methods for analyzing protein interaction networks to uncover protein function. Our methods exploit the topological structure of interaction networks in order to make predictions, and can be applied to either experimentally or computationally determined protein interaction maps.