Fundamentals and Methods for T- and B-Cell Epitope Prediction

Table 2

Selected B-cell epitope prediction methods available for free online use.

Tool	Method	Server (URL)	Ref.
Linear B cell epitope
PEOPLE	Propensity scale method	http://www.iedb.org/	[103]
BepiPred	ML (DT)	http://www.cbs.dtu.dk/services/BepiPred/	[110]
ABCpred	ML (ANN)	http://www.imtech.res.in/raghava/abcpred/	[111]
LBtope	ML (ANN)	http://www.imtech.res.in/raghava/lbtope/	[112]
BCPREDS	ML (SVM)	http://ailab.ist.psu.edu/bcpred/	[113]
SVMtrip	ML (SVM)	http://sysbio.unl.edu/SVMTriP/prediction.php	[114]
Conformational B-cell epitope
CEP	Structure-based method (solvent accessibility)	http://bioinfo.ernet.in/cep.htm	[118]
DiscoTope	Structure-based method (surface accessibility and propensity amino acid score)	http://tools.iedb.org/discotope/	[119]
ElliPro	Structure-based method (geometrical properties)	http://tools.iedb.org/ellipro/	[121]
PEPITO	Structure-based method (physicochemical properties and geometrical structure)	http://pepito.proteomics.ics.uci.edu/	[122]
SEPPA	Structure-based method (physicochemical properties and geometrical structure)	http://lifecenter.sgst.cn/seppa/	[123]
EPITOPIA	Structure-based method (ML-naïve Bayes)	http://epitopia.tau.ac.il/	[125]
EPSVR	Structure-based method (ML-SVR)	http://sysbio.unl.edu/EPSVR/	[126]
EPIPRED	Structure-based method (ASEP, Docking)	http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/EpiPred.php	[129]
PEASE	Structure-based method (ASEP, ML)	http://www.ofranlab.org/PEASE	[130]
MIMOX	Mimotope	http://immunet.cn/mimox/helps.html	[131]
PEPITOPE	Mimotope	http://pepitope.tau.ac.il/	[132]
EpiSearch	Mimotope	http://curie.utmb.edu/episearch.html	[133]
MIMOPRO	Mimotope	http://informatics.nenu.edu.cn/MimoPro	[134]
CBTOPE	Sequence based (SVM)	http://www.imtech.res.in/raghava/cbtope/submit.php	[136]