MHC-I binding predictions

MHC-I processing predictions

Processing

Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, and Holzhutter HG. 2005. Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci. 62:1025-1037.
PMID: 15868101

Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG. 2003. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol. 171:1741-1749.
PMID: 12902473

ANN

Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, and Nielsen M. 2008. NetMHC-3.0: Accurate web accessible predictions of Human, Mouse, and Monkey MHC class I affinities for peptides of length 8-11. NAR 36:W509-512.
PMID: 18463140

Lundegaard C, Nielsen M, Lund O. 2006. The validity of predicted T-cell epitopes. Trends Biotechnol 24:537-538.
PMID: 17045685

Lundegaard C, Lund O, and Nielsen M. 2008. Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioinformatics 24:1397-1398.
PMID: 18413329

Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O. 2003. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci 12:1007-1017.
PMID: 12717023

Buus S, Lauemøller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S. 2003. Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 62:378-384.
PMID: 14617044

SMM

Peters B, Sette A. 2005. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 6:132.
PMID: 15927070

ARB

Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothé BR, Chisari FV, Watkins DI, Sette A. 2005. Immunogenetics 57:304-314.
PMID: 15868141

NetMHCpan

Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Roder G, Peters B, Sette A, Lund O, Buus S. 2007. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS ONE 2:e796.
PMID: 17726526