title: Predicting the structure of protein-protein complexes using the SwarmDock Web Server.
abstract: 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.
authors.affiliation: Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, UK.
authors.forename: Mieczyslaw
authors.initials: M
authors.lastname: Torchala
authors.forename: Paul A
authors.initials: PA
authors.lastname: Bates
mesh_terms: D008958:Models, Molecular; D062105:Molecular Docking Simulation; D046912:Multiprotein Complexes / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D064878:Web Browser
chemical_list: D046912:Multiprotein Complexes; D011506:Proteins