Transducing environmental signals from the cell surface to the nucleus in order to evoke appropriate gene regulatory response requires an accurate and robust medium to propagate biological information. The structure of proteins and especially the dynamic properties of these structures allows for the uptake and restitution of biological information from and to the environment. To understand the functioning and regulation of signalling pathways we therefore have to understand how protein structures encode biological information. Towards this goal several computational methods have been carried out over the last years. First we will provide an overview of these in silico approaches. Next, using the well known SH2 domain as a case study, we describe two specific approaches in more detail to illustrate the similarities and differences between sequence-based and structure-based methods for the analysis of protein communication. Both methods address the same question yet from a different level of description. As a consequence both have their limits and a number of pros and cons that are discussed here. Together all the methods discussed here provide an arsenal of in silico approaches that may be used to understand how information content is maintained through protein structural dynamics, elucidating explicitly information transfer in signalling networks.