메뉴 건너뛰기




Volumn 197, Issue 6, 2016, Pages 2492-2499

Unsupervised HLA peptidome deconvolution improves ligand prediction accuracy and predicts cooperative effects in peptide-HLA interactions

Author keywords

[No Author keywords available]

Indexed keywords

HLA ANTIGEN; PEPTIDE; HLA ANTIGEN CLASS 1; LIGAND; PEPTIDOMIMETIC AGENT; PROTEIN BINDING;

EID: 84988940043     PISSN: 00221767     EISSN: 15506606     Source Type: Journal    
DOI: 10.4049/jimmunol.1600808     Document Type: Article
Times cited : (94)

References (41)
  • 1
    • 0032718484 scopus 로고    scopus 로고
    • Identification of naturally processed and HLA-presented Epstein-Barr virus peptides recognized by CD4(+) or CD8(+) T lymphocytes from human blood
    • Herr, W., E. Ranieri, A. Gambotto, L. S. Kierstead, A. A. Amoscato, L. Gesualdo, and W. J. Storkus. 1999. Identification of naturally processed and HLA-presented Epstein-Barr virus peptides recognized by CD4(+) or CD8(+) T lymphocytes from human blood. Proc. Natl. Acad. Sci. USA 96: 12033-12038.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 12033-12038
    • Herr, W.1    Ranieri, E.2    Gambotto, A.3    Kierstead, L.S.4    Amoscato, A.A.5    Gesualdo, L.6    Storkus, W.J.7
  • 8
    • 84959881509 scopus 로고    scopus 로고
    • Gapped sequence alignment using artificial neural networks: Application to the MHC class i system
    • Andreatta, M., and M. Nielsen. 2016. Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics 32: 511-517.
    • (2016) Bioinformatics , vol.32 , pp. 511-517
    • Andreatta, M.1    Nielsen, M.2
  • 11
    • 25444476693 scopus 로고    scopus 로고
    • Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
    • Peters, B., and A. Sette. 2005. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 6: 132.
    • (2005) BMC Bioinformatics , vol.6 , pp. 132
    • Peters, B.1    Sette, A.2
  • 12
    • 82255164138 scopus 로고    scopus 로고
    • Towards a systems understanding of MHC class i and MHC class II antigen presentation
    • Neefjes, J., M. L. M. Jongsma, P. Paul, and O. Bakke. 2011. Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat. Rev. Immunol. 11: 823-836.
    • (2011) Nat. Rev. Immunol. , vol.11 , pp. 823-836
    • Neefjes, J.1    Jongsma, M.L.M.2    Paul, P.3    Bakke, O.4
  • 16
    • 84894283785 scopus 로고    scopus 로고
    • A comprehensive analysis of constitutive naturally processed and presented HLA-C04:01 (Cw4)-specific peptides
    • Schittenhelm, R. B., N. L. Dudek, N. P. Croft, S. H. Ramarathinam, and A. W. Purcell. 2014. A comprehensive analysis of constitutive naturally processed and presented HLA-C04:01 (Cw4)-specific peptides. Tissue Antigens 83: 174-179.
    • (2014) Tissue Antigens , vol.83 , pp. 174-179
    • Schittenhelm, R.B.1    Dudek, N.L.2    Croft, N.P.3    Ramarathinam, S.H.4    Purcell, A.W.5
  • 17
    • 84948702563 scopus 로고    scopus 로고
    • Analysis of major histocompatibility complex (MHC) immunopeptidomes using mass spectrometry
    • Caron, E., D. J. Kowalewski, C. Chiek Koh, T. Sturm, H. Schuster, and R. Aebersold. 2015. Analysis of major histocompatibility complex (MHC) immunopeptidomes using mass spectrometry. Mol. Cell. Proteomics 14: 3105-3117.
    • (2015) Mol. Cell. Proteomics , vol.14 , pp. 3105-3117
    • Caron, E.1    Kowalewski, D.J.2    Koh, C.C.3    Sturm, T.4    Schuster, H.5    Aebersold, R.6
  • 20
    • 84871811905 scopus 로고    scopus 로고
    • Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach
    • Andreatta, M., O. Lund, and M. Nielsen. 2013. Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. Bioinformatics 29: 8-14.
    • (2013) Bioinformatics , vol.29 , pp. 8-14
    • Andreatta, M.1    Lund, O.2    Nielsen, M.3
  • 21
    • 84924326106 scopus 로고    scopus 로고
    • Mass spectrometry of human leukocyte antigen class i peptidomes reveals strong effects of protein abundance and turnover on antigen presentation
    • Bassani-Sternberg, M., S. Pletscher-Frankild, L. J. Jensen, and M. Mann. 2015. Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Mol. Cell. Proteomics 14: 658-673.
    • (2015) Mol. Cell. Proteomics , vol.14 , pp. 658-673
    • Bassani-Sternberg, M.1    Pletscher-Frankild, S.2    Jensen, L.J.3    Mann, M.4
  • 23
    • 84966661138 scopus 로고    scopus 로고
    • Highsensitivity HLA class i peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients' sera
    • Ritz, D., A. Gloger, B. Weide, C. Garbe, D. Neri, and T. Fugmann. 2016. Highsensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients' sera. Proteomics 16: 1570-1580.
    • (2016) Proteomics , vol.16 , pp. 1570-1580
    • Ritz, D.1    Gloger, A.2    Weide, B.3    Garbe, C.4    Neri, D.5    Fugmann, T.6
  • 25
    • 84859303311 scopus 로고    scopus 로고
    • MUSI: An integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets
    • Kim, T., M. S. Tyndel, H. Huang, S. S. Sidhu, G. D. Bader, D. Gfeller, and P. M. Kim. 2012. MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. Nucleic Acids Res. 40: e47.
    • (2012) Nucleic Acids Res. , vol.40 , pp. E47
    • Kim, T.1    Tyndel, M.S.2    Huang, H.3    Sidhu, S.S.4    Bader, G.D.5    Gfeller, D.6    Kim, P.M.7
  • 29
    • 84910121126 scopus 로고    scopus 로고
    • Uncovering the peptide-binding specificities of HLA-C: A general strategy to determine the specificity of any MHC class i molecule
    • Rasmussen, M., M. Harndahl, A. Stryhn, R. Boucherma, L. L. Nielsen, F. A. Lemonnier, M. Nielsen, and S. Buus. 2014. Uncovering the peptide-binding specificities of HLA-C: a general strategy to determine the specificity of any MHC class I molecule. J. Immunol. 193: 4790-4802.
    • (2014) J. Immunol. , vol.193 , pp. 4790-4802
    • Rasmussen, M.1    Harndahl, M.2    Stryhn, A.3    Boucherma, R.4    Nielsen, L.L.5    Lemonnier, F.A.6    Nielsen, M.7    Buus, S.8
  • 31
    • 44649189266 scopus 로고    scopus 로고
    • Prediction of peptide-MHC binding using profiles
    • Reche, P. A., and E. L. Reinherz. 2007. Prediction of peptide-MHC binding using profiles. Methods Mol. Biol. 409: 185-200.
    • (2007) Methods Mol. Biol. , vol.409 , pp. 185-200
    • Reche, P.A.1    Reinherz, E.L.2
  • 32
    • 0026529908 scopus 로고
    • HLA-A2-peptide complexes: Refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides
    • Garboczi, D. N., D. T. Hung, and D. C. Wiley. 1992. HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. Proc. Natl. Acad. Sci. USA 89: 3429-3433.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 3429-3433
    • Garboczi, D.N.1    Hung, D.T.2    Wiley, D.C.3
  • 34
    • 84947042013 scopus 로고    scopus 로고
    • Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
    • Andreatta, M., E. Karosiene, M. Rasmussen, A. Stryhn, S. Buus, and M. Nielsen. 2015. Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification. Immunogenetics 67: 641-650.
    • (2015) Immunogenetics , vol.67 , pp. 641-650
    • Andreatta, M.1    Karosiene, E.2    Rasmussen, M.3    Stryhn, A.4    Buus, S.5    Nielsen, M.6
  • 35
    • 84958568837 scopus 로고    scopus 로고
    • The length distribution of class I-restricted T cell epitopes is determined by both peptide supply and MHC allele-specific binding preference
    • Trolle, T., C. P. McMurtrey, J. Sidney, W. Bardet, S. C. Osborn, T. Kaever, A. Sette, W. H. Hildebrand, M. Nielsen, and B. Peters. 2016. The length distribution of class I-restricted T cell epitopes is determined by both peptide supply and MHC allele-specific binding preference. J. Immunol. 196: 1480-1487.
    • (2016) J. Immunol. , vol.196 , pp. 1480-1487
    • Trolle, T.1    McMurtrey, C.P.2    Sidney, J.3    Bardet, W.4    Osborn, S.C.5    Kaever, T.6    Sette, A.7    Hildebrand, W.H.8    Nielsen, M.9    Peters, B.10
  • 37
    • 84962905590 scopus 로고    scopus 로고
    • NetMHCpan-3.0; Improved prediction of binding to MHC class i molecules integrating information from multiple receptor and peptide length datasets
    • Nielsen, M., and M. Andreatta. 2016. NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med. 8: 33.
    • (2016) Genome Med. , vol.8 , pp. 33
    • Nielsen, M.1    Andreatta, M.2
  • 39
    • 84923611798 scopus 로고    scopus 로고
    • Revisiting the arthritogenic peptide theory: Quantitative not qualitative changes in the peptide repertoire of HLA-B27 allotypes
    • Schittenhelm, R. B., T. C. C. L. K. Sian, P. G. Wilmann, N. L. Dudek, and A. W. Purcell. 2015. Revisiting the arthritogenic peptide theory: quantitative not qualitative changes in the peptide repertoire of HLA-B27 allotypes. Arthritis Rheumatol. 67: 702-713.
    • (2015) Arthritis Rheumatol. , vol.67 , pp. 702-713
    • Schittenhelm, R.B.1    Sian, T.C.C.L.K.2    Wilmann, P.G.3    Dudek, N.L.4    Purcell, A.W.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.