Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design

Table 3 Mean error (kcal/mol) for the binding free energies with CASA and GB/SA

data set	number of mutations^b	CASA	GB-ACE	GB-HCT	reference
all^a	55 (52/48)	1.76	2.39	1.96	[66–72]
charged^a	24 (23/20)	2.09	2.70	2.89
AspRS	9 (9/9)	1.86	3.40	1.25	[73]
TyrRS	15 (15/15)	0.62	0.80	1.13	[66–70]
Lyso	9 (9/7)	2.68	3.01	2.92	[71]
CD4	22 (19/17)	1.89	2.34	2.53	[72]
BPTI^c	25	2.75	-	-	[38, 39]

^aExcluding the BPTI complexes, which were computed with a slightly different protocol and for which GB data are not available. ^bFor GB-ACE and GB-HCT, some mutations were excluded due to unfavorable VdW contacts; the numbers of mutations (ACE/HCT) are in parentheses. ^cBPTI:trypsin and :chymotrypsin complexes.

ISSN: 1471-2105