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

Table 1

Selected T-cell epitope prediction tools available online for free public use.

Tool	URL	Method^1	MHC class	A	S	T	P	Ref.
EpiDOCK	http://epidock.ddg-pharmfac.net	SB	II	—	—	—	—	[86]
MotifScan	https://www.hiv.lanl.gov/content/immunology/motif_scan/motif_scan	SM	I and II	—	X	—	—	—
Rankpep	http://imed.med.ucm.es/Tools/rankpep.html	MM	I and II	—	—	—	X	[26]
SYFPEITHI	http://www.syfpeithi.de/	MM	I and II	—	—	—	—	[23]
MAPPP	http://www.mpiib-berlin.mpg.de/MAPPP/	MM	I	—	X	—	X	[87]
PREDIVAC	http://predivac.biosci.uq.edu.au/	MM	II	—	—	—	—	[88]
PEPVAC	http://imed.med.ucm.es/PEPVAC/	MM	I	—	X	—	X	[63]
EPISOPT	http://bio.med.ucm.es/episopt.html	MM	I	—	X	—	—	[64]
Vaxign	http://www.violinet.org/vaxign/	MM	I and II	—	—	—	—	[89]
MHCPred	http://www.ddg-pharmfac.net/mhcpred/MHCPred/	QSAR	I and II	X	—	—	—	[34]
EpiTOP	http://www.pharmfac.net/EpiTOP	QSAR	II	X	—	—	—	[90]
BIMAS	https://www-bimas.cit.nih.gov/molbio/hla_bind/	QAM	I	X				[28]
TEPITOPE	http://datamining-iip.fudan.edu.cn/service/TEPITOPEpan/TEPITOPEpan.html	QAM	II	X	—	—	—	[32]
Propred	http://www.imtech.res.in/raghava/propred/	QAM	II	X	X	—	—	[91]
Propred-1	http://www.imtech.res.in/raghava/propred1/	QAM	I	X	X	—	X	[92]
EpiJen	http://www.ddg-pharmfac.net/epijen/EpiJen/EpiJen.htm	QAM	I	X	—	X	X	[82]
IEDB-MHCI	http://tools.immuneepitope.org/mhci/	Combined	I	X	—	—	—	[93]
IEDB-MHCII	http://tools.immuneepitope.org/mhcii/	Combined	II	X	—	—	—	[93]
IL4pred	http://webs.iiitd.edu.in/raghava/il4pred/index.php	SVM	II	—	—	—	—	[67]
MULTIPRED2	http://cvc.dfci.harvard.edu/multipred2/index.php	ANN	I and II	—	X	—	—	[62]
MHC2PRED	http://www.imtech.res.in/raghava/mhc2pred/index.html	SVM	II	—	—	—	—	[38]
NetMHC	http://www.cbs.dtu.dk/services/NetMHC/	ANN	I	X	—	—	—	[49]
NetMHCII	http://www.cbs.dtu.dk/services/NetMHCII/	ANN	II	X	—	—	—	[30]
NetMHCpan	http://www.cbs.dtu.dk/services/NetMHCpan/	ANN	I	X	—	—	—	[54]
NetMHCIIpan	http://www.cbs.dtu.dk/services/NetMHCIIpan/	ANN	II	X	—	—	—	[55]
nHLApred	http://www.imtech.res.in/raghava/nhlapred/	ANN	I	—	—	—	X	[94]
SVMHC	http://abi.inf.uni-tuebingen.de/Services/SVMHC/	SVM	I and II	—	—	—	—	[95]
SVRMHC	http://us.accurascience.com/SVRMHCdb/	SVM	I and II	X	—	—	—	[46]
NetCTL	http://www.cbs.dtu.dk/services/NetCTL/	ANN	I	X	X	X	X	[83]
WAPP	https://abi.inf.uni-tuebingen.de/Services/WAPP/index_html	SVM	I	—	—	X	X	[37]

¹Method used for prediction of peptide-MHC binding. Keys for methods: SM: sequence motif; SB: structure-based; MM: motif matrix; QAM: quantitative affinity matrix; SVM: support vector machine; ANN: artificial neural network; QSAR: quantitative structure-activity relationship model; combined: tool uses different methods including ANN and QAM, selecting the more appropriate method for each distinct MHC molecule. The table also indicates whether the tools predict quantitative binding affinity (A), supertypes (S), TAP binding (T), and proteasomal cleavage (P); marked with an X in the affirmative case.