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
Links to video presentation on SciVee site:
http://www.scivee.tv/node/4651 - NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence (paper in Plos One)