Figure 2From: Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDockBest cluster rank docking results of redocking of the PDB entry 2FDP. Protein surfaces are colored by partial charges (a, PM6 charges, RMSD from coordinates in PDB: 0.75 b, Gasteiger charges, RMSD from coordinates in PDB: 2.35). The darker color of the protein surface colored by PM6 partial charges as compared to the colors of Figure 2b reflects the higher calculated absolute value of semi-empirical partial charges. This "sharper" surface defines the possible binding geometry of the ligand more, than in the case of Gasteiger charges.Back to article page