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Table 1 FPocketWeb/fpocket benchmarks

From: FPocketWeb: protein pocket hunting in a web browser

PDB

Protein

FPocketWeb Time (s)

fpocket Time (s)

Score

1HWL [20]

HMG-CoA reductase

5.6 ± 0.095

5.1 ± 0.149

0.437

2P16 [21]

factor Xa

0.7 ± 0.032

0.6 ± 0.009

0.961

3LN1 [22]

COX-2

15.9 ± 0.514

16.0 ± 0.145

0.630

4LL3 [23]

HIV protease

0.4 ± 0.052

0.3 ± 0.015

0.862

4TZ4

Cereblon

5.2 ± 0.048

5.3 ± 0.075

0.301

  1. Times are reported in seconds. FPocketWeb and fpocket produced the same scores; we report the scores associated with the top-ranked pockets. The calculations were performed on PDB files downloaded directly from the Protein Data Bank, without further processing.