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Figure 2 | Journal of Cheminformatics

Figure 2

From: Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

Figure 2

Best 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.

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