Table 2.

Correlation coefficients and RMSE of AlGDock free energies with respect to YANK. The AlGDock free energies were calculated using different sets of receptor snapshots, obtained from separate YANK simulations for ligands (i) to (vi) in complex with T4 Lysozyme.

Snapshots used in AlGDock Calculations	Pearson’s R w.r.t. YANK	RMSE w.r.t. YANK (kcal/mol)
all 576 snapshots	0.90 (0.02)	1.59 (0.23)
384 active snapshots	0.88 (0.01)	1.74 (0.22)
i) methylpyrrole	0.77 (0.03)	3.29 (0.35)
ii) benzene	0.72 (0.03)	4.27 (0.45)
iii) xylene	0.86 (0.01)	1.96 (0.32)
iv) phenol	0.19 (0.02)	5.06 (0.77)
v) n-hexylbenzene	0.63 (0.03)	4.75 (0.47)
vi) (±)-camphor	0.91 (0.01)	1.87 (0.15)