MHC-I binding predictions

MHC-I binding predictions - Reference

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

SMMPMBEC

Kim Y, Sidney J, Pinilla C, Sette A, Peters B. 2009. Derivation of an Amino Acid Similarity Matrix for Peptide:MHC Binding and Its Application as a Bayesian Prior. To be published

ARB

Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothé BR, Chisari FV, Watkins DI, Sette A. 2005. Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 57:304-314.
PMID: 15868141

CombLib

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

Consensus

Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A. 2006. A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol 24:817-819.
PMID: 16767078

NetMHCpan

Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M. 2009. NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61:1-13.
PMID: 19002680

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