Methods to reveal domain networks.

The development and application of high-throughput technology to study protein interactions has led to the construction of complex interaction maps, the correct interpretation of which is crucial to the identification of targets for drug development. Here we propose that a more informative description of protein interaction networks can be achieved by considering explicitly the modular nature of proteins. In this representation, proteins are drawn as covalently linked modular domains binding to their target sites in partner proteins. Families of conserved modules that bind to relatively short peptides mediate a large fraction of the non-covalent interactions linking different proteins in the network. As these interactions are often involved in the propagation of signal transduction, determining the recognition specificity of each domain family member is an essential step toward a functional description of the global interactome.