On the Virtues of Automated QSAR ‒ The New Kid on the Block
Best models generated with AutoQSAR for each disease
S1-S4
RESULTS. Table S1. Alzheimer’s disease (hBACE1) best models generated with AutoQSAR for each training set. Overall best model is highlighted Training set, %
Model
Score
Q²
R²
SD
RMSE
t, min
70
KPLS_desc_7
0.83
0.82
0.83
0.45
0.41
55
71
KPLS_radial_25
0.80
0.82
0.83
0.44
0.44
55
72
KPLS_Dendritic_13
0.85
0.82
0.85
0.42
0.40
55
73
KPLS_molprint2D_1
0.85
0.83
0.87
0.39
0.38
55
74
KPLS_molprint2D_44
0.86
0.84
0.88
0.38
0.37
55
75
PLS_50
0.83
0.85
0.83
0.44
0.42
55
76
KPLS_molprint2D_42
0.88
0.89
0.88
0.38
0.31
55
77
KPLS_molprint2D_11
0.83
0.80
0.83
0.44
0.42
55
78
KPLS_molprint2D_11
0.83
0.80
0.83
0.44
0.42
55
79
KPLS_dendritic_21
0.86
0.85
0.86
0.41
0.35
55
80
KPLS_radial_36
0.88
0.87
0.88
0.37
0.36
55
Table S2. Asthma (hBACE1) best models generated with AutoQSAR for each training set. Overall best model is highlighted. Training set, %
Model
Score
Q²
R²
SD
RMSE
t, min
70
MLR_14
0.73
0.75
0.76
0.52
0.51
39
71
KPLS_desc_28
0.76
0.79
0.75
0.52
0.48
39
72
KPLS_desc_28
0.76
0.79
0.75
0.52
0.48
39
73
KPLS_radial_16
0.75
0.79
0.74
0.52
0.47
39
74
KPLS_dendritic_26
0.76
0.82
0.89
0.34
0.43
39
75
KPLS_dendritic_26
0.76
0.82
0.89
0.34
0.43
39
76
KPLS_desc_37
0.77
0.78
0.77
0.51
0.49
39
77
KPLS_radial_4
0.82
0.85
0.82
0.45
0.42
39
78
KPLS_radial_4
0.82
0.85
0.82
0.45
0.42
39
79
KPLS_radial_18
0.87
0.88
0.87
0.39
0.34
39
80
KPLS_radial_18
0.87
0.88
0.87
0.39
0.34
39
S1
Table S3. Cardiovascular (ABHD6) best models generated with AutoQSAR for each training set. Overall best model is highlighted. Training set, %
Model
Score
Q²
R²
SD
RMSE
t, min
70
MLR_42
0.54
0.67
0.50
0.68
0.59
22
71
KPLS_dendritic_39
0.75
0.69
0.75
0.50
0.47
22
72
KPLS_dendritic_39
0.75
0.69
0.75
0.50
0.47
22
73
KPLS_dendritic_39
0.75
0.69
0.75
0.50
0.47
22
74
KPLS_dendritic_30
0.73
0.71
0.73
0.52
0.47
22
75
KPLS_dendritic_30
0.73
0.71
0.73
0.52
0.47
22
76
KPLS_dendritic_30
0.73
0.71
0.73
0.52
0.47
22
77
KPLS_linear_13
0.73
0.71
0.72
0.52
0.46
22
78
KPLS_linear_13
0.73
0.71
0.72
0.52
0.46
22
79
KPLS_desc_19
0.72
0.70
0.74
0.50
0.49
22
80
KPLS_desc_19
0.72
0.70
0.74
0.50
0.49
22
Table S4. Chagas disease (cruzain) best models generated with AutoQSAR for each training set. Overall best model is highlighted. Training set, %
Model
Score
Q²
R²
SD
RMSE
t, min
70
KPLS_molprint2D_29
0.87
0.87
0.88
0.36
0.35
32
71
KPLS_molprint2D_32
0.87
0.87
0.87
0.37
0.35
32
72
KPLS_molprint2D_32
0.87
0.87
0.87
0.37
0.35
32
73
KPLS_desc_35
0.86
0.87
0.90
0.35
0.35
32
74
KPLS_molprint2D_30
0.84
0.84
0.87
0.37
0.38
32
75
KPLS_molprint2D_30
0.84
0.84
0.87
0.37
0.38
32
76
KPLS_desc_45
0.89
0.89
0.89
0.35
0.32
32
77
KPLS_desc_45
0.89
0.89
0.89
0.35
0.32
32
78
KPLS_desc_23
0.85
0.88
0.90
0.33
0.36
32
79
KPLS_desc_23
0.84
0.87
0.90
0.34
0.36
32
80
KPLS_desc_23
0.84
0.87
0.90
0.34
0.36
32
S2
Table S5. Diabetes (PTP1B) best models generated with AutoQSAR for each training set. Overall best model is highlighted. Training set, %
Model
Score
Q²
R²
SD
RMSE
t, min
70
KPLS_molprint2D_20
0.81
0.90
0.80
0.34
0.25
12
71
KPLS_molprint2D_20
0.81
0.90
0.80
0.34
0.25
12
72
KPLS_molprint2D_46
0.76
0.74
0.75
0.40
0.32
12
73
KPLS_molprint2D_46
0.76
0.74
0.75
0.40
0.32
12
74
KPLS_molprint2D_46
0.76
0.74
0.75
0.40
0.32
12
75
KPLS_linear_27
0.86
0.83
0.86
0.31
0.26
12
76
KPLS_linear_27
0.86
0.83
0.86
0.31
0.26
12
77
KPLS_molprint2D_30
0.86
0.91
0.86
0.29
0.24
12
78
KPLS_molprint2D_30
0.86
0.91
0.86
0.29
0.24
12
79
KPLS_molprint2D_30
0.86
0.91
0.86
0.29
0.24
12
80
KPLS_dendritic_22
0.89
0.86
0.89
0.27
0.24
12
Table S6. Malaria (PfDHODH) best models generated with AutoQSAR for each training set. Overall best model is highlighted. Training set, %
Model
Score
Q²
R²
SD
RMSE
t, min
70
PLS_12
0.76
0.77
0.78
0.52
0.52
97
71
KPLS_desc_35
0.82
0.82
0.82
0.47
0.46
97
72
KPLS_desc_7
0.81
0.81
0.81
0.48
0.47
97
73
KPLS_desc_50
0.82
0.83
0.84
0.45
0.45
97
74
KPLS_desc_7
0.81
0.81
0.82
0.47
0.47
97
75
KPLS_desc_22
0.81
0.83
0.81
0.48
0.46
97
76
KPLS_desc_37
0.77
0.79
0.81
0.49
0.50
140
77
KPLS_desc_48
0.81
0.81
0.80
0.49
0.47
97
78
KPLS_desc_26
0.83
0.84
0.82
0.47
0.44
97
79
KPLS_desc_20
0.83
0.84
0.84
0.44
0.44
97
80
KPLS_desc_11
0.85
0.85
0.85
0.44
0.43
97
S3
Table S7. Schistosomiasis (SmTGR) best models generated with AutoQSAR for each training set. Overall best model is highlighted. Training set, %
