AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
A) Translational points. The surface enclosing points of the carbon affinity map located outside the protein and with carbon affinity less than or equal to -0.3 kcal/mol is shown in blue; protein atomic spheres (with reduced vdW radii) are shown in green. The set of translational points cover grooves and cavities that can accommodate a ligand and provide sensible initial placement points for the ligand root atom. B) Translational points cutoff value selection For energy cutoff values varying from 0.0 to -0.6 kcal/mol in decrements of 0.1 kcal/mol, the average number of grid points retained is plotted against the average number of retained grid points within 1Å of the ligand root atom. The average is computed over the 85 systems in the Astex Diverse set. Lower energy cutoff values produce fewer translational points, however they increase the chance of discarding points surrounding the ligand root atom (i.e. reducing coverage of the root). The value of -0.3 kcal/mol is the closest to the curve’s inflection point and was selected as the best cutoff value to maximize the reduction in retained points and maximize the coverage of the ligand root atom.