Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility

We present a series of molecular-mechanics-based protein refinement methods, including two novel ones, applied as part of an induced fit docking procedure. The methods used include minimization; protein and ligand sidechain prediction; a hierarchical ligand placement procedure similar to a-priori protein loop predictions; and a minimized Monte Carlo approach using normal mode analysis as a move step. The results clearly indicate the importance of a proper opening of the active site backbone, which might not be accomplished when the ligand degrees of freedom are prioritized. The most accurate method consisted of the minimized Monte Carlo procedure designed to open the active site followed by a hierarchical optimization of the sidechain packing around a mobile flexible ligand. The methods have been used on a series of 88 protein-ligand complexes including both cross-docking and apo-docking members resulting in complex conformations determined to within 2.0 A heavy-atom RMSD in 75% of cases where the protein backbone rearrangement upon binding is less than 1.0 A alpha-carbon RMSD. We also demonstrate that physics-based all-atom potentials can be more accurate than docking-style potentials when complexes are sufficiently refined.