HIV protease (N= 112)
|
Trypsin (N= 73)
|
---|
Scoring function
|
R
p
1
|
R
s
2
|
SD
3
|
RMSE4
|
D5
|
Scoring function
|
R
p
1
|
R
s
2
|
SD
3
|
RMSE4
|
D5
|
---|
X-Score::HPScore
|
0.341
|
0.339
|
1.54
|
1.509
|
N
|
SYBYL::ChemScore
|
0.829
|
0.773
|
0.95
|
-
|
U
|
BsN::XARG
|
0.290
|
0.230
|
1.56
|
1.705
|
Y
|
DS::Ludi2
|
0.823
|
0.791
|
0.96
|
-
|
U
|
RF::XARG
|
0.289
|
0.219
|
1.519
|
1.719
|
Y
|
X-Score::HSScore
|
0.817
|
0.824
|
0.97
|
1.401
|
N
|
BgN-Score::XARG
|
0.287
|
0.209
|
1.58
|
1.860
|
Y
|
DS::PLP2
|
0.797
|
0.774
|
1.02
|
-
|
U
|
SYBYL::ChemScore
|
0.255
|
0.228
|
1.58
|
-
|
U
|
BgN-Score::XAR
|
0.776
|
0.719
|
1.06
|
1.070
|
Y
|
DrugScore::PairSurf
|
0.225
|
0.170
|
1.59
|
-
|
U
|
RF::XAR
|
0.774
|
0.753
|
1.07
|
1.133
|
Y
|
DS::PMF04
|
0.183
|
0.200
|
1.61
|
-
|
U
|
BsN-Score::AR
|
0.766
|
0.709
|
1.08
|
1.119
|
Y
|
SNN-Score::X
|
0.039
|
0.048
|
1.64
|
2.255
|
Y
|
SNN-Score::X
|
0.735
|
0.672
|
1.14
|
1.209
|
Y
|
RF::XARG
|
0.964
|
0.975
|
0.44
|
0.588
|
N
|
BsN-Score::XARG
|
0.937
|
0.920
|
0.59
|
0.678
|
N
|
BsN-Score::XARG
|
0.918
|
0.922
|
0.64
|
0.710
|
N
|
RF::XARG
|
0.934
|
0.08
|
0.60
|
0.657
|
N
|
BgN-Score::XARG
|
0.848
|
0.808
|
1.02
|
1.024
|
N
|
BgN-Score::XARG
|
0.892
|
0.848
|
0.76
|
0.805
|
N
|
SNN-Score::X
|
0.748
|
0.716
|
1.08
|
1.085
|
N
|
SNN-Score::X
|
0.829
|
0.789
|
0.940
|
0.957
|
N
|
Carbonic anhydrase (
N
= 44)
|
Thrombin (
N
= 38)
|
Scoring function
|
R
p
1
|
R
s
2
|
SD
3
|
RMSE
4
|
D
5
|
Scoring function
|
R
p
1
|
R
s
2
|
SD
3
|
RMSE
4
|
D
5
|
DS::PLP2
|
0.800
|
0.772
|
0.84
|
-
|
U
|
SNN-Score::X
|
0.756
|
0.704
|
1.38
|
1.433
|
Y
|
SYBYL::G-Score
|
0.706
|
0.646
|
0.99
|
-
|
U
|
BgN-Score::XARG
|
0.722
|
0.726
|
1.48
|
1.552
|
Y
|
SYBYL::ChemScore
|
0.699
|
0.631
|
1.00
|
-
|
U
|
BsN-Score::XARG
|
0.699
|
0.637
|
1.58
|
1.603
|
Y
|
BsN-Score::X
|
0.674
|
0.434
|
1.03
|
3.418
|
Y
|
RF::XARG
|
0.697
|
0.693
|
1.52
|
1.674
|
Y
|
SNN-Score::X
|
0.631
|
0.451
|
1.08
|
3.561
|
Y
|
DS::PLP1
|
0.667
|
0.672
|
1.58
|
-
|
U
|
SYBYL::PMF-Score
|
0.627
|
0.618
|
1.09
|
-
|
U
|
SYBYL::G-Score
|
0.667
|
0.626
|
1.58
|
-
|
U
|
BgN-Score::XA
|
0.625
|
0.423
|
1.09
|
3.642
|
Y
|
X-Score::HSScore
|
0.666
|
0.586
|
1.58
|
1.737
|
N
|
RF::XARG
|
0.601
|
0.374
|
1.11
|
3.393
|
Y
|
DrugScore::Pair
|
0.651
|
0.622
|
1.61
|
-
|
U
|
BsN-Score::XARG
|
0.948
|
0.921
|
0.44
|
1.004
|
N
|
BsN-Score::XARG
|
0.913
|
0.938
|
0.86
|
1.155
|
N
|
RF::XARG
|
0.910
|
0.860
|
0.57
|
1.140
|
N
|
RF::XARG
|
0.910
|
0.934
|
0.86
|
1.125
|
N
|
BgN-Score::XARG
|
0.884
|
0.766
|
0.65
|
1.320
|
N
|
BgN-Score::XARG
|
0.858
|
0.876
|
1.08
|
1.320
|
N
|
SNN-Score::X
|
0.652
|
0.310
|
1.05
|
1.687
|
N
|
SNN-Score::X
|
0.761
|
0.756
|
1.37
|
1.374
|
N
|
- 1 R
p
is the Pearson correlation coefficient between predicted and measured BA values of complexes in this protein-family-specific test set.
- 2 R
s
is the Spearman correlation coefficient between predicted and measured BA values of complexes in this protein-family-specific test set.
- 3 SD is the standard deviation of errors between predicted and measured BA values of complexes in this protein-family-specific test set.
- 4 RMSE is the root-mean-square of errors between predicted and measured BA values of the test complexes in in this protein-family-specific test set. Test RMSE is not available for conventional SFs except for X-Score that we have re-constructed. Training RMSE is not reported in this table because the values are very similar to RMSEtrain in Table 1 due to the overlap between the training data sets of the two experiments.
- 5 This indicates whether the test set complexes are disjoint from (D = Y) or overlap with (D = N) the training set complexes for NN and RF models. Any overlap between the training and test data of the conventional SFs is unknown (D = U) to us.