Table 1: List of online tools for T-cell epitope prediction.

ToolWebsiteTypeClassRefs

ANNPREDhttp://www.imtech.res.in/raghava/nhlapred/neural.htmlANNI[234]
Bimashttp://www-bimas.cit.nih.gov/molbio/hla_bind/QMI[51]
EpiJenhttp://www.ddg-pharmfac.net/epijen/EpiJen/EpiJen.htmMulti-step algorithmI[235]
EPIMHChttp://imed.med.ucm.es/epimhc/user made ProfilesI, II[236]
EpiMatrixhttp://www.epivax.com/Matrix-based and pocket profileI, II[237]
HLABINDhttp://atom.research.microsoft.com/hlabinding/hlabinding.aspxAdaptive Double ThreadingI[238]
IEDBhttp://tools.immuneepitope.org/analyze/html/mhc_binding.htmlARB-QM, SMM-QM, ANN-regressionI[239]
KISShttp://cbio.ensmp.fr/kiss/SVMI[240]
MHC2PREDhttp://www.imtech.res.in/raghava/mhc2pred/SVMII[241]
MHC Predhttp://www.jenner.ac.uk/MHCPredPartial least-squares-based multivariate statistical methodI, II[242]
MULTIPREDhttp://antigen.i2r.a-star.edu.sg/multipred/ANN, pHMMI, II[243]
MOTIF_SCANhttp://www.hiv.lanl.gov/content/immunology/motif_scan/motif_scanSequence MotifsI, II
NetCTLhttp://www.cbs.dtu.dk/services/NetCTL/Multi-step algorithmI, CTL[60]
NetCTLSpanhttp://www.cbs.dtu.dk/services/NetCTLpan/Multi-step algorithmI, CTL[62]
NetMHChttp://www.cbs.dtu.dk/services/NetMHC/ANNI[244]
netMHCIIhttp://www.cbs.dtu.dk/services/NetMHCII/SMM-QMII[245]
netMHCpanhttp://www.cbs.dtu.dk/services/NetMHCpan/ANN-regressionI[246]
netMHCIIpanhttp://www.cbs.dtu.dk/services/NetMHCIIpan/ANN-regressionII[247]
PEPVAChttp://imed.med.ucm.es/PEPVAC/Profiles or PSSMI[248]
PREDEPhttp://margalit.huji.ac.il/Teppred/mhc-bind/index.htmlThreadingI[249]
POPIhttp://iclab.life.nctu.edu.tw/POPI/SVMI, II[250]
PROPREDIhttp://www.imtech.res.in/raghava/propred1/QMI[251]
PROPREDhttp://www.imtech.res.in/raghava/propred/QMII[252]
RANKPEPhttp://imed.med.ucm.es/Tools/rankpep.htmlProfiles or PSSMI, II[253]
SVMHChttp://abi.inf.uni-tuebingen.de/SVMHCSVMI, II[254]
SVRMHChttp://svrmhc.biolead.org/SVM-regressionI, II[255]
SYFPEITHIhttp://www.syfpeithi.de/Motif matricesI, II[50]
TEPITOPEhttp://www.vaccinome.com/QMII[256]
Vaxignhttp://www.violinet.org/vaxign/PSSMI, II[110]

Abbreviations: ANN: artificial neural networks; PSSM: position-specific scoring matrix; QM: quantitative matrices; SMM: stabilized matrix method; SVM: support vector machine; multistep algorithm: integrating predictions of proteasomal cleavage, TAP transport efficiency, and MHC class I affinity.