Chapter 3: Modeling Protein–Protein Interactions by Rigid-body Docking

Protein–protein interactions and the formation of protein–protein complexes are central to many biological processes. Protein docking is the task of calculating the three-dimensional structure of a protein complex starting from the individual structures of the constituent proteins. Although proteins are intrinsically flexible, most docking algorithms begin by assuming that the proteins to be docked are rigid. This assumption allows fast rigid-body docking techniques to be used to generate a relatively small list of candidate docking poses which may subsequently be refined using more computationally intensive force-field based approaches. Protein docking predictions are helping to provide a better physical picture of protein–protein interactions, and the use of protein docking is becoming an increasingly important way to help identify potential drug targets. This chapter gives an overview of current theory and practice in the use of computational and data-based protein docking techniques, with particular focus on using fast Fourier transform techniques and modern graphics processors to accelerate the rigid body part of a docking calculation.