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:

Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M. 2018. NN-align. Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology 154(3):394-406.
PMID: 29315598 Download PDF

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:

Reynisson B., Alvarez B., Paul S., Peters B., Nielsen M. 2020. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 48(W1):W449-W454.
PMID: 32406916 Download PDF

Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M. 2018. Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology 154(3):394-406.
PMID: 29315598 Download PDF

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