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Table 2 Prediction speed

From: P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure

Method

Time†

COACH (web server)

15 h (self reported estimate)

eFindSite (web server)

\(6.9\pm 0\) h

COACH (stand-alone)

\(6.4\pm 2\) h

GalaxySite (web server)

2 h (self reported estimate)

3DLigandSite (web server)

1–3 h (self reported estimate)

ISMBLab-LIG (web server)

\(71\pm 2\) min

FTSite (web server)

\(39\pm 3\) min

LISE (web server)

\(39\pm 0.1\) min

MetaPocket 2.0 (web server)

\(2.8\pm 0.4\) min

DeepSite (web server)

\(38\pm 0.03\) s

SiteHound (stand-alone)

\(12\pm 0.5\) s

P2Rank (stand-alone)

\(6.8\pm 0.2\) s (cold start*)

 

0.9 s (in larger dataset*)

Fpocket (stand-alone)

\(0.2\pm 0.01\) s

  1. †Average time required for LBS prediction on a single protein. Displayed is self reported estimate or a result of our test on a small dataset of 5 proteins á \(\sim \)2500 atoms. Stand-alone tools were tested on a single 3.7 GHz CPU core. For web servers the wall time from submitting a job to receiving the result was measured.
  2. *Difference is due to JVM initialization and model loading cost
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Journal of Cheminformatics

ISSN: 1758-2946

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