DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

Table 4 Pearson correlation coefficients and root mean squared error between experimental binding affinity and binding affinity predicted by DLIGAND, DLIGAND2, and X-Score using docking poses generated by eight docking programs along with the results from the docking programs

Docking program	Pearson correlation coefficient				Root mean squared error
Docking program	Self	DLIGAND	DLIGAND2	X-Score	Self	DLIGAND	DLIGAND2	X-Score
AutoDock	0.404	0.465	0.537	0.547	1.91	1.77	1.69	1.68
AutoDock Vina	0.501	0.459	0.519	0.536	1.74	1.78	1.72	1.69
rDock	0.102	0.463	0.535	0.507	2.01	1.78	1.70	1.76
LeDock	0.426	0.457	0.532	0.54	1.82	1.78	1.69	1.69
UCSF DOCK	0.195	0.427	0.498	0.488	1.97	1.81	1.74	1.76
iDock	0.485	0.461	0.522	0.54	1.75	1.78	1.71	1.69
GalaxyDock	0.487	0.464	0.537	0.532	1.75	1.78	1.69	1.71
iGEMDOCK	0.384	0.444	0.501	0.502	1.85	1.80	1.76	1.82
Average	0.373	0.455	0.523	0.524	1.85	1.79	1.71	1.73

ISSN: 1758-2946