Table 1.

Availability, features and category of the computational functional site prediction tools discussed in this work.

Name	Category	URL	Features
Evolutionary Trace	Sequence-and-structure based	http://mammoth.bcm.tmc.edu/ETserver.html	Web-server, also available as Stand-alone version
ConSurf	Sequence, Sequence + structure	http://consurf.tau.ac.il	Web-server
MINER	Sequence	http://miniminer.sourceforge.net	Stand-alone version
FREPS (DSPAC index)	Sequence-and-structure based	http://freps.cbrc.jp	Appropriate Selection of homologous sequences, Web-server
ProBis	Structure based	http://probis.cmm.ki.si	Local structure alignment + geometry, Web-server + Stand-alone
FINDSITE	Structure based	http://cssb.biology.gatech.edu/findsite	Global structure alignment, Web-server
COFACTOR	Structure based	http://zhanglab.ccmb.med.umich.edu/COFACTOR/	Global + local structure alignment, web-server
LIGSITE	Structure-based	http://projects.biotec.tu-dresden.de/pocket	Geometric, Superseded by LIGSITEcsc server
LIGSITEcsc	Structure-based	http://projects.biotec.tu-dresden.de/pocket/	Geometric, Web-server + stand alone
SURFNET	Structure-based	http://www.ebi.ac.uk/thornton-srv/software/SURFNET/	Geomertric, Stand-alone
Q-SiteFinder	Structure-based	http://www.modelling.leeds.ac.uk/qsitefinder/	Energetic, Web-server
Pocket-Finder	Structure-based	http://www.modelling.leeds.ac.uk/pocketfinder/	Energetic, Web-server
FOD	Structure-based	http://bioinformatics.cm-uj.krakow.pl/activesite/	Energetic, Web-server
FTSite	Structure-based	http://ftsite.bu.edu	Energetic, Web-server
ConCavity	Sequence-and-structure based	http://compbio.cs.princeton.edu/concavity/	Web-server + Stand-alone
SURFNET-ConSurf	Sequence-and-structure-based	Not available	Global + local structure alignement
MetaPocket	Structure-based	http://projects.biotec.tu-dresden.de/pocket/	Meta-approach, Web-server