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Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding.

Ray S, Kepler TB.

Immunome Res. 2007 Oct 29;3:9.PMID: 17967170 [PubMed - in process]Related articlesFree article

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.

Nielsen M, Lundegaard C, Lund O.

BMC Bioinformatics. 2007 Jul 4;8:238.PMID: 17608956 [PubMed - indexed for MEDLINE]Related articlesFree article

Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research.

Lin HH, Zhang GL, Tongchusak S, Reinherz EL, Brusic V.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S22.PMID: 19091022 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of genomewide conserved epitope profiles of HIV-1: classifier choice and peptide representation.

Xiao Y, Segal MR.

Stat Appl Genet Mol Biol. 2005;4:Article25. Epub 2005 Sep 16.PMID: 16646843 [PubMed]Related articlesFree article

NetMHCpan, a method for MHC class I binding prediction beyond humans.

Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M.

Immunogenetics. 2009 Jan;61(1):1-13. Epub 2008 Nov 12.PMID: 19002680 [PubMed - indexed for MEDLINE]Related articles

Improving peptide-MHC class I binding prediction for unbalanced datasets.

Sales AP, Tomaras GD, Kepler TB.

BMC Bioinformatics. 2008 Sep 19;9:385.PMID: 18803836 [PubMed - indexed for MEDLINE]Related articlesFree article

Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan.

Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O.

PLoS Comput Biol. 2008 Jul 4;4(7):e1000107.PMID: 18604266 [PubMed - indexed for MEDLINE]Related articlesFree article

Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research.

Lin HH, Ray S, Tongchusak S, Reinherz EL, Brusic V.

BMC Immunol. 2008 Mar 16;9:8.PMID: 18366636 [PubMed - indexed for MEDLINE]Related articlesFree article

Genomewide conserved epitope profiles of HIV-1 predicted by biophysical properties of MHC binding peptides.

Sung MH, Simon R.

J Comput Biol. 2004;11(1):125-45.PMID: 15072692 [PubMed - indexed for MEDLINE]Related articles

Predicting affinity and specificity of antigenic peptide binding to major histocompatibility class I molecules.

Sieker F, May A, Zacharias M.

Curr Protein Pept Sci. 2009 Jun;10(3):286-96. Review.PMID: 19519456 [PubMed - indexed for MEDLINE]Related articles

Shift-invariant adaptive double threading: learning MHC II-peptide binding.

Zaitlen N, Reyes-Gomez M, Heckerman D, Jojic N.

J Comput Biol. 2008 Sep;15(7):927-42.PMID: 18771399 [PubMed - indexed for MEDLINE]Related articles

Non-natural and photo-reactive amino acids as biochemical probes of immune function.

Gómez-Nuñez M, Haro KJ, Dao T, Chau D, Won A, Escobar-Alvarez S, Zakhaleva V, Korontsvit T, Gin DY, Scheinberg DA.

PLoS One. 2008;3(12):e3938. Epub 2008 Dec 15.PMID: 19079589 [PubMed - indexed for MEDLINE]Related articlesFree article

Peptide length significantly influences in vitro affinity for MHC class II molecules.

O'Brien C, Flower DR, Feighery C.

Immunome Res. 2008 Nov 26;4:6.PMID: 19036163 [PubMed - in process]Related articlesFree article

Ranking of binding and nonbinding peptides to MHC class I molecules using inverse folding approach: Implications for vaccine design.

Singh SP, Mishra BN.

Bioinformation. 2008;3(2):72-82. Epub 2008 Oct 24.PMID: 19238199 [PubMed - in process]Related articlesFree article

A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach.

Wang P, Sidney J, Dow C, Mothé B, Sette A, Peters B.

PLoS Comput Biol. 2008 Apr 4;4(4):e1000048.PMID: 18389056 [PubMed - indexed for MEDLINE]Related articlesFree article

A community resource benchmarking predictions of peptide binding to MHC-I molecules.

Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, Kostem E, Basch D, Lamberth K, Harndahl M, Fleri W, Wilson SS, Sidney J, Lund O, Buus S, Sette A.

PLoS Comput Biol. 2006 Jun 9;2(6):e65. Epub 2006 Jun 9.PMID: 16789818 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms.

Rajapakse M, Schmidt B, Feng L, Brusic V.

BMC Bioinformatics. 2007 Nov 22;8:459.PMID: 18031584 [PubMed - indexed for MEDLINE]Related articlesFree article

Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity: in silico bioinformatic step-by-step guide using quantitative structure-activity relationships.

Hattotuwagama CK, Doytchinova IA, Flower DR.

Methods Mol Biol. 2007;409:227-45.PMID: 18450004 [PubMed - indexed for MEDLINE]Related articles

In silico prediction of peptide-MHC binding affinity using SVRMHC.

Liu W, Wan J, Meng X, Flower DR, Li T.

Methods Mol Biol. 2007;409:283-91.PMID: 18450008 [PubMed - indexed for MEDLINE]Related articles

Major histocompatibility complex class II molecule-human immunodeficiency virus peptide analysis using a microarray chip.

Gaseitsiwe S, Valentini D, Ahmed R, Mahdavifar S, Magalhaes I, Zerweck J, Schutkowski M, Gautherot E, Montero F, Ehrnst A, Reilly M, Maeurer M.

Clin Vaccine Immunol. 2009 Apr;16(4):567-73. Epub 2009 Feb 18.PMID: 19225081 [PubMed - indexed for MEDLINE]Related articlesFree article