Modeling Protein Docking Using Polar Fourier Correlations and Case-Based Reasoning

ProteinProtein-protein interactions (PPIs) and the formation of protein-protein complexes are central to many biological processes. Protein docking is the task of calculating the three-dimensional (3D) structure of a protein complex starting from the two individual structures of the component proteins. In this talk, I will give an overview of my "Hex" polar Fourier correlation docking algorithm, and I will briefly describe how the calculations may be accelerated using modern graphics processor units (GPUs). Then I will describe some recent work on using a knowledge-based approach to the docking problem called “KBDOCK”. Briefly, KBDOCK collects all known hetero domain interactions from the Protein DataBank and combines and clusters them by Pfam family. This allows known protein binding sites to be re-used as 3D docking “templates” in what is effectively a case-based reasoning approach to the docking problem. We find that protein domains belonging to the same Pfam family often interact in similar ways. Hence, when suitable examples exist in the case base, KBDOCK provides a near-perfect way to provide high quality templates which may subsequently be refined using a combination of rigid body and flexible docking algorithms. Hex and KBDOCK are available at http://hex.loria.fr and http://kbdock.loria.fr respectively