IEDB Analysis Resource

References

Consensus:
Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B. 2010. Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics. 11:568.
PMID: 21092157 Download PDF

Wang P, Sidney J, Dow C, Mothé B, Sette A, Peters B. 2008. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol. 4(4):e1000048.
PMID: 18389056 Download PDF

NN-align:
Nielsen M, Lund O. 2009. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics. 10:296.
PMID: 19765293 Download PDF

SMM-align:
Nielsen M, Lundegaard C, Lund O. 2007. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics. 8:238.
PMID: 17608956 Download PDF

Combinatorial library:
Sidney J, Assarsson E, Moore C, Ngo S, Pinilla C, Sette A, Peters B. 2008. Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res 4:2.
PMID: 18221540

Sturniolo:
Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, Braxenthaler M, Gallazzi F, Protti MP, Sinigaglia F, Hammer J. 1999. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol. 17(6):555-561.
PMID: 10385319 Download PDF

NetMHCIIpan:
Andreatta M, Karosiene E, Rasmussen M, Stryhn A, Buus S, and Nielsen M. 2015. Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification. Immunogenetics.67(11-12):641-50.
PMID: 26416257 Download PDF