Table 4 Average AUC-ROC and AUC-PR scores for 5 repetitions of 5 fold cv. on each of the four data sets. The standard deviations are given in parenthesis

Enzyme

SIMCOMP

0.863 (0.016)

0.303 (0.027)

413,7 min

Edit

0.833 (0.016)

0.178 (0.004)

6

NLCS

0.837 (0.014)

0.228 (0.013)

4

CLCS

0.834 (0.013)

0.234 (0.019)

331

SMILES-based substring

0.752 (0.006)

0.169 (0.010)

133

SMIfp CBD (34D)

0.846 (0.009)

0.199 (0.008)

1

SMIfp Tanimoto (34D)

0.832 (0.012)

0.191 (0.012)

1

SMIfp CBD (38D)

0.852 (0.009)

0.205 (0.009)

1

SMIfp Tanimoto (38D)

0.844 (0.012)

0.201 (0.006)

1

LINGOsim (q =3)

0.846 (0.013)

0.290 (0.013)

3

LINGOsim (q =4)

0.823 (0.010)

0.294 (0.006)

3

LINGOsim (q =5)

0.819 (0.015)

0.264 (0.013)

3

LINGO-based TF

0.811 (0.017)

0.259 (0.008)

19

LINGO-based TF-IDF

0.822 (0.012)

0.292 (0.031)

47

TF-IDF+SIMCOMP

0.852 (0.010)

0.348 (0.017) ^a

LINGOsim+SIMCOMP

0.852 (0.016)

0.318 (0.019) ^a

Ion Channels

SIMCOMP

0.776 (0.012)

0.224(0.032)

48,7 min

Edit

0.754 (0.013)

0.199 (0.025)

1

NLCS

0.753 (0.007)

0.189 (0.037)

0,9

CLCS

0.755 (0.018)

0.185 (0.028)

47

SMILES-based substring

0.743 (0.004)

0.197 (0.031)

21

SMIfp CBD (34D)

0.717 (0.019)

0.136 (0.036)

0,3

SMIfp Tanimoto (34D)

0.698 (0.015)

0.125 (0.022)

0,3

SMIfp CBD (38D)

0.722 (0.012)

0.137 (0.024)

0,3

SMIfp Tanimoto (38D)

0.699 (0.028)

0.156 (0.028)

0,4

LINGOsim (q =3)

0.737 (0.015)

0.192 (0.046)

0,8

LINGOsim (q =4)

0.737 (0.011)

0.197 (0.037)

1

LINGOsim (q =5)

0.727 (0.009)

0.188 (0.026)

1

LINGO-based TF

0.738 (0.018)

0.204 (0.024)

3

LINGO-based TF-IDF

0.712 (0.014)

0.178 (0.029)

7

TF-IDF+SIMCOMP

0.763 (0.010)

0.234 (0.017)

LINGOsim+SIMCOMP

0.773 (0.012)

0.229 (0.018)

GPCR

SIMCOMP

0.867 (0.009)

0.307 (0.018)

71,2 min

Edit

0.844 (0.015)

0.248 (0.030)

1

NLCS

0.853 (0.006)

0.247 (0.013)

1

CLCS

0.855 (0.014)

0.279 (0.030)

52

SMILES-based substring

0.782 (0.019)

0.205 (0.032)

21

SMIfp CBD (34D)

0.852 (0.014)

0.209 (0.018)

0,3

SMIfp Tanimoto (34D)

0.847 (0.006)

0.213 (0.016)

0,3

SMIfp Tanimoto (38D)

0.856 (0.009)

0.228 (0.015)

0,3

LINGOsim (q =3)

0.875 (0.003)

0.317 (0.015)

1

LINGOsim (q =4)

0.876 (0.004)

0.333 (0.020) ^a

1

LINGOsim (q =5)

0.874 (0.006) ^a

0.337 (0.019) ^a

1

LINGO-based TF

0.872 (0.004)

0.335 (0.012) ^a

3

LINGO-based TF-IDF

0.871 (0.007)

0.348 (0.018) ^a

9

TF-IDF+SIMCOMP

0.885 (0.006) ^a

0.371 (0.017) ^a

LINGOsim+SIMCOMP

0.879 (0.009) ^a

0.335 (0.016) ^a

Nuclear Receptors

SIMCOMP

0.856 (0.015)

0.435 (0.008)

2,9 min

Edit

0.828 (0.009)

0.305 (0.029)

0,2

NLCS

0.815 (0.018)

0.302 (0.032)

0,2

CLCS

0.813 (0.037)

0.319 (0.039)

10

SMILES-based substring

0.766 (0.028)

0.335 (0.035)

2

SMIfp CBD (34D)

0.809 (0.026)

0.296 (0.015)

0,1

SMIfp Tanimoto (34D)

0.784 (0.031)

0.281 (0.020)

0,1

SMIfp CBD (38D)

0.815 (0.017)

0.307 (0.024)

0,1

SMIfp Tanimoto (38D)

0.787 (0.030)

0.322 (0.034)

0,1

LINGOsim (q =3)

0.800 (0.013)

0.351 (0.036)

0,2

LINGOsim (q =4)

0.829 (0.013)

0.414 (0.031)

0,2

LINGOsim (q =5)

0.834 (0.013)

0.389 (0.023)

0,2

LINGO-based TF

0.820 (0.013)

0.373 (0.035)

0,4

LINGO-based TF-IDF

0.855 (0.022)

0.418 (0.016)

0,8

TF-IDF+SIMCOMP

0.861 (0.008)

0.436 (0.049)

LINGOsim+SIMCOMP

0.840 (0.015)

0.399 (0.031)