Table 1 Attributes of and citations for the epitope prediction programs used

ARB

Average relative binding matrices

[42] (59)

[43]

MHCPred

Partial least squares

[33] (46)

[44]

[34] (30)

[35] (30)

ProPred

Matrix-based

TEPITOPE matrices; requires key anchor residues

[45] (186)

[41]

TEPITOPE: [30] (310)

RankPep

Position Specific

[23] (119)

[47]

Scoring Matrices

[46] (102)

NetMHCII

Position Specific Scoring Matrices

Predicts epitopes of multiple lengths; uses SMM-align matrices

[37] (29)

[48]

SVRMHC

Support vector machine regression

[32] (16)

[49]

[31] (23)

Vaxign

Position Specific Scoring Matrices

[40] (0)

[50]

NetMHCIIpan

Artificial Neural Networks

Predicts multiple-length epitope binding to every sequenced Class II allele

[11] (3)

[51]