Skip to main content

Table 1 Evaluation of SiteHopper retrieval of binding site patches from the sc-PDB (2013) belonging to the same protein as a query patch

From: Mapping the 3D structures of small molecule binding sites

 

N (sc-PDB)

AUROC

EF (5%)

BEDROC

ligCav

 BRD4 (n = 2)

15

1.00 ± 0.00

20.03 ± 0.00

1.00 ± 0.00

 Carbonic anhydrase 2 (n = 3)

76

1.00 ± 0.00

19.77 ± 0.00

0.99 ± 0.00

 CDK2 (n = 3)

180

1.00 ± 0.00

19.66 ± 0.07

0.97 ± 0.01

 Estrogen receptor (n = 5)

58

1.00 ± 0.00

20.03 ± 0.00

0.96 ± 0.01

 HIV-1 protease (n = 3)

219

0.99 ± 0.00

19.94 ± 0.00

0.99 ± 0.00

 Prothrombin (n = 3)

126

1.00 ± 0.00

20.03 ± 0.00

1.00 ± 0.00

fpocket

 BRD4 (n = 2)

15

0.97 ± 0.03

18.67 ± 1.33

0.94 ± 0.06

 Carbonic anhydrase 2 (n = 3)

76

0.99 ± 0.00

18.69 ± 0.00

0.93 ± 0.00

 CDK2 (n = 3)

180

0.76 ± 0.03

8.83 ± 1.74

0.43 ± 0.10

 Estrogen receptor (n = 5)

58

0.94 ± 0.01

16.07 ± 0.17

0.80 ± 0.01

 HIV-1 protease (n = 3)

219

0.98 ± 0.00

19.52 ± 0.00

0.97 ± 0.00

 Prothrombin (n = 3)

126

0.94 ± 0.01

17.76 ± 0.32

0.88 ± 0.01

  1. Comparison between the ligCav dataset of ligand-dependent binding sites (N = 9275), and those identified through fpocket cavity detection (N = 24,345). Mean results and standard errors are shown. n = number of queries; for further detail of the query and true positive patches see Additional file 1: Table S1