Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

Table 5

Binding energies (in kcal/mol) calculated as   −    −  , where and are energies of the protein-ligand complex and the free ligand in their global minima, respectively, and is energy of the protein in its configuration prepared as it is described in Section 2. The global energies of complexes and ligands were taken from respective minima sets (see Section 2.2). is the experimental binding energy calculated from the binding constant. “Energy range” is the difference between the highest and the lowest energies among all 16 protein-ligand complexes. “Energy correlation” is Pearson correlation coefficient between experimental and calculated binding energies. Autodock and SOL scoring functions are also given to compare (in kcal/mol).

PDB ID		MMFF94	MMFF94 + PCM	PM7	PM7 + COSMO	MMFF94	MMFF94 + PCM	MMFF94 + SGB	Sol Score	Autodock score
4FT0	−10.1	63.84	0.04	−39.48	−48.67	58.64	−0.08	3.03	−5.20	−7.15
4FT9	−10.9	−63.72	−9.98	−111.64	−48.77	−64.83	−10.05	−16.34	−4.29	−4.9
4FSW	−6.8	−60.20	−5.89	−108.48	−46.41	−60.19	−6.53	−7.72	−4.78	−6.08
4FTA	−9.8	−30.36	−5.44	−126.54	−58.61	−30.35	−15.04	−14.05	−4.35	−4.7
4FV5	−10.9	−102.01	−7.42	−168.44	−54.37	−102.01	−4.64	−11.16	−6.05	−8.25
4FV6	−12.3	−96.92	−7.75	−164.91	−72.68	−89.27	−13.42	−13.87	−5.26	−5.6
1DWC	−10.5	−146.16	−33.43	−194.69	−70.12	−144.88	−32.93	−36.77	−2.86	−4.24
1TOM	−11.8	−248.29	−49.66	−258.10	−73.67	−248.28	−49.89	−51.59	−8.11	−7.88
1C5Y	−6.0	−34.83	−79.15	−33.81	−52.84	−34.83	−79.34	−80.85	−6.83	−5.28
1F5L	−7.5	17.40	−52.26	−29.98	−81.95	17.40	−52.54	−52.88	−4.41	−6.62
1O3P	−9.4	3.59	−40.30	−32.53	−64.60	3.59	−40.59	−42.54	−6.95	−8.43
1SQO	−10.6	−24.78	−50.42	−58.75	−69.56	−24.78	−51.30	−52.22	−6.75	−8.68
1VJ9	−10.7	−49.57	−50.03	−91.69	−76.58	−49.20	−43.77	−49.18	−4.53	−3.17
1VJA	−10.9	−49.87	−51.91	−95.43	−81.40	−47.97	−38.86	−41.85	−4.47	−1.82
2P94	−13.0	−68.20	−15.74	−153.53	−68.94	−67.28	−15.79	−20.87	−6.53	−13.09
3CEN	−11.7	−69.48	−18.17	−133.10	−63.12	−69.47	−18.43	−26.62	−5.48	−11.68
Energy range	7.0	312	79.2	228	35.5	306.93	79.26	83.89	5.25	11.27
Energy correlation		0.41	−0.36	0.60	0.33	0.40	−0.39	−0.35	0.09	0.13