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.
KeywordsSwarmDock Protein–protein complexes Protein–protein interactions Protein docking Protein structure prediction
This work was funded by Cancer Research UK. We are grateful to Iain Moal and Raphael Chaleil for their fruitful collaborations on the subject of modelling protein–protein interactions.
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