Predicting the structure of protein-protein complexes using the SwarmDock Web Server.

Protein-protein interactions drive many of the biological functions of the cell. Any two proteins have the potential to interact; however, whether the interactions are of biological significance is dependent on a number of complicated factors. Thus, modelling the three-dimensional structure of protein-protein complexes is still considered to be a complex endeavor. Nevertheless, many experimentalists now wish to boost their knowledge of protein-protein interactions, well beyond complexes resolved experimentally, and for them to be able to do so it is important they are able to effectively and confidently predict protein-protein interactions. The main aim of this chapter is to acquaint the reader, particularly one from a non-computational background, how to use a state-of-the-art protein docking tool. In particular, we describe here the SwarmDock Server (SDS), a web service for the flexible modelling of protein-protein complexes; this server is freely available at: http://bmm.cancerresearchuk.org/~SwarmDock/. Supplementary files for Case Studies are provided with the chapter and available at extras.springer.com.