The functional dynamics of signal transduction through protein interaction networks are determined both by network topology and by the signal processing properties of component proteins. In order to understand the emergent properties of signal transduction networks in terms of information processing, storage and decision making, we not only need to map the so-called 'interactome' but, perhaps more importantly, we also have to understand how the structural dynamics of constituent proteins shape non-linear responses through cooperativity and allostery. Several in silico methods have been developed to identify networks of cooperative residues in proteins and help infer their mode of action. Applying this type of analysis to important classes of modular signal transduction domains should, in principle, allow the function of these proteins to be abstracted in terms of their information processing characteristics, permitting better comprehension of the systemic properties of biological networks.