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Table 1 Availability of existing tools for ligand binding site prediction from protein structure introduced since 2009

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

Name Year Type Web server Stand-alone Fully automated Source Code
SiteMap [35] 2009 Geometric Yes Yes
Fpocket [18] 2009 Geometric Yes Yes Yes Yes
SiteHound [28] 2009 Energetic Yes Yes Yes Yes
ConCavity [36] 2009 Conservation Yes Yes Yes
3DLigandSite [37] 2010 Template Yes
POCASA [38] 2010 Geometric Yes
DoGSite [39] 2010 Geometric Yes
MetaPocket 2.0 [27] 2011 consensus Yes
MSPocket [81] 2011 Geometric Yes Yes Yes
FTSite [40] 2012 Energetic Yes
LISE [41] 2012 Knowledge/conservation Yes Yes
COFACTOR [42] 2012 Template Yes Yes Yes
COACH [43] 2013 Template Yes Yes Yes
G-LoSA [44] 2013 Template Yes Yes
eFindSite [45] 2013 Template Yes Yes Yes
GalaxySite [46] 2014 Template/docking Yes
LIBRA [47] 2015 Template Yes Yes
P2Rank (this work) 2015* Machine learning –** Yes Yes Yes
bSiteFinder [48] 2016 Template Yes
ISMBLab-LIG [32] 2016 Machine learning Yes
DeepSite [33] 2017 Machine learning Yes
  1. Applies to stand-alone versions
  2. ††Consensus of template based methods: TM-SITE, S-SITE and COFACTOR (also FINDSITE and ConCavity in web version)
  3. *Algorithm introduced in conference proceedings [49]
  4. **In development