. Author manuscript; available in PMC: 2018 Jan 22.

Published in final edited form as: J Chem Inf Model. 2016 Nov 18;56(12):2388–2400. doi: 10.1021/acs.jcim.6b00362

Table 5.

Statistics for MM-GB/SA Results^a

		rigid receptor			5 Å sampling

protein system	protein structure	R²^b	slope^b	PI	R²^b	slope	PI
RD4	3mxf	0.44 [0.08,0.75]	6.50 [±2.72]	0.61	0.48 [0.11,0.77]	5.69 [±2.44]	0.63
	hm-3s91	0.42 [0.06,0.74]	5.22 [±2.47]	0.58	0.48 [0.11,0.77]	4.95 [±2.51]	0.56
	hm-3oni	0.43 [0.07,0.74]	5.44 [±2.27]	0.64	0.43 [0.07,0.74]	6.55 [±2.75]	0.56
MCL-1	4hw3	0.30 [0.00,0.73]	10.13 [±4.40]	0.59	0.27 [0.01,0.72]	8.96 [±4.31]	0.57
	hm-2nl9	0.00 [0.00,0.34]	−0.86 [±4.53]	−0.03	0.10 [0.11,0.58]	3.40 [±3.73]	0.46
	hm-4lvt	0.25 [0.01,0.70]	3.84 [±2.91]	0.61	0.41 [0.01,0.79]	9.49 [±3.81]	0.67
Tyk2	4gih	0.49 [0.08,0.80]	2.77 [±1.78]	0.70	0.32 [0.00,0.70]	1.72 [±1.67]	0.55
	hm-3eyg	0.10 [0.06,0.52]	1.05 [±1.84]	0.34	0.13 [0.04,0.55]	1.24 [±1.87]	0.55
	hm-3eqr	0.12 [0.05,0.54]	1.20 [±1.91]	0.33	0.01 [0.20,0.35]	0.26 [±1.64]	0.16
	hm-1byg	0.02 [0.17,0.38]	0.49 [±1.91]	0.25	0.06 [0.10,0.46]	0.79 [±1.90]	0.28
	3nyx	0.65 [0.24,0.87]	3.18 [±1.65]	0.84	0.22 [0.00,0.63]	1.06 [±1.51]	0.51
A_2A	4eiy	0.48 [0.00,0.87]	6.06 [±3.10]	0.55	0.30 [0.04,0.80]	5.48 [±3.54]	0.37
	hm-4amj	0.49 [0.00,0.87]	8.29 [±3.56]	0.58	0.63 [0.07,0.91]	16.01 [±4.30]	0.73

In both runs the ligand was minimized. In the second series of calculations protein residues within 5 Å of the ligand were sampled using the hierarchical sampling procedure in Prime MM-GB/SA.⁶⁵

Error intervals at a 95% confidence limit are calculated according to the work of Nicholls.⁷²