Modelling Protein–Protein and Protein–DNA Docking

This chapter contains sections titled: Introduction The need for protein–protein and protein–DNA docking Overview of the computational approach Scope of this chapter Structural studies of protein complexes Methodology of a protein–protein docking strategy Rigid body docking by Fourier correlation theory Use of residue pair potentials to re-rank docked complexes Use of distance constraints Refinement and additional screening of complexes Implementation of the docking suite Results from the protein–protein docking strategy Modelling protein–DNA complexes Method Results Strategies for protein–protein docking Evaluation of the results of docking simulations Fourier correlation methods Other rigid-body docking approaches Flexible protein–protein docking Rigid-body treatment to re-rank putative docked complexes Introduction of flexibility to re-rank putative docked complexes Blind trials of protein–protein docking Energy landscape for protein docking Conclusions