Table 2
Performance of PBSA and GBSA in selected studies
Reference
Target
Sample size Elec. model ϵ
S
a
Weighted terms
b
Entropy method
ΔG
Performance
__Null
d
__
range
c
mue rmse R
mue rmse
Ligands: small molecules
[48]
Avidin
9
PB
1 SA
NM
[À5.0;À20.4] 3.3 3.8
0.96 4.1 4.9
[49]
HIV-I protease 12
PB
?
SA
NM
[À11.9;
À7.8] 1.1 1.2
0.74 1.1 1.3
[50]
DHFR
22
PB
1 SA
NM
[À15.0;
À5.5] 7.2 8.0
0.91 2.4 2.7
[50]
DHFR
22
GB
1 SA
NM
[À15.0;
À5.5] 16.4 18.0 0.94 2.4 2.7
[51]
Alpha-thrombin 7
PB
4 SA
NM
[À12.4;
À4.0] 19.8 20.7 0.80 2.1 2.6
[51]
Avidin
7
PB
1 SA
NM
[À20.4;
À4.5] 7.8 8.1
0.93 4.7 5.3
[51]
Cytochrome C 18
PB
1 SA
NM
[À7.1;
À3.8] 11.9 12.4 0.30 0.7 0.8
[51]
Neuraminidase 8
PB
4 SA
NM
[À11.5;
À3.7] 2.3 2.9
0.68 2.2 2.6
[51]
P450cam
9
PB
1 SA
NM
[À7.9;
À5.5] 5.8 6.1
0.68 0.8 0.9
[51]
Penicillopepsin 7
PB
2 SA
NM
[À12.8;
À6.8] 2.8 3.0
0.41 2.1 2.3
[52]
HIV-I protease 20
PB
1 PB, vdW, SA, TS NM
[À16.5;
À9.9] 1.0 1.2
0.72 1.8 2.0
[52]
FXa
20
PB
1 PB, vdW, SA, TS NM
[À12.8;
À8.6] 0.6 0.8
0.54 0.8 1.5
[52]
Hsp90
16
PB
1 PB, vdW, SA, TS NM
[À10.5;
À5.1] 1.2 1.4
0.63 1.6 1.8
Ligands: peptidomimetics
[53]
MMP-2
8
PB
1 PB, vdW, SA
NM
[À15.0;
À7.8] 3.0 3.6
0.84 1.9 2.2
Ligands: RNA
[54]
RNA aptamer
5
PB
1 SA
–
[1.1; 5.6]
3.5 3.8
0.66 1.2 1.5
[55]
RNA aptamer
6
PB
?
SA
NM
[À11.5;
À6.0] 6.5 6.6
0.75 1.2 1.7
(continued)
Computational Design of Binding
251