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Volumn 22, Issue 13, 2006, Pages 1648-1655

Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules

Author keywords

[No Author keywords available]

Indexed keywords

HLA A ANTIGEN; HLA A1 ANTIGEN; HLA A2 ANTIGEN; HLA A24 ANTIGEN; HLA A3 ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN;

EID: 33745593748     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl141     Document Type: Article
Times cited : (35)

References (53)
  • 1
    • 0030811688 scopus 로고    scopus 로고
    • Human histocompatibility leukocyte antigen-binding supermotifs predict broadly cross-reactive cytotoxic T lymphocyte responses in patients with acute hepatitis
    • Bertoni,R. et al. (1997) Human histocompatibility leukocyte antigen-binding supermotifs predict broadly cross-reactive cytotoxic T lymphocyte responses in patients with acute hepatitis. J. Clin. Invest., 100, 503-513.
    • (1997) J. Clin. Invest. , vol.100 , pp. 503-513
    • Bertoni, R.1
  • 2
    • 0032532306 scopus 로고    scopus 로고
    • Human class I supertypes and CTL repertoires extend to chimpanzees
    • Bertoni,R. et al. (1998) Human class I supertypes and CTL repertoires extend to chimpanzees. J. Immunol., 161, 4447-4455.
    • (1998) J. Immunol. , vol.161 , pp. 4447-4455
    • Bertoni, R.1
  • 3
    • 0037461027 scopus 로고    scopus 로고
    • MHCBN: A comprehensive database of MHC binding and non-binding peptides
    • Bhasin,M. et al. (2003) MHCBN: A comprehensive database of MHC binding and non-binding peptides. Bioinformatics, 19, 665-666.
    • (2003) Bioinformatics , vol.19 , pp. 665-666
    • Bhasin, M.1
  • 4
    • 0036211926 scopus 로고    scopus 로고
    • JenPep: A database of quantitative functional peptide data for immunology
    • Blythe,M.J. et al. (2002) JenPep: A database of quantitative functional peptide data for immunology.. Bioinformatics, 118, 434-439.
    • (2002) Bioinformatics , vol.118 , pp. 434-439
    • Blythe, M.J.1
  • 5
    • 0031825709 scopus 로고    scopus 로고
    • Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network
    • Brusic,V. et al. (1998a) Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. Bioinformatics, 14, 121-130.
    • (1998) Bioinformatics , vol.14 , pp. 121-130
    • Brusic, V.1
  • 6
    • 0031811850 scopus 로고    scopus 로고
    • MHCPEP, a database of MHC-binding peptides: Update 1997
    • Brusic,V. et al. (1998b) MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res., 26, 368-371.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 368-371
    • Brusic, V.1
  • 9
    • 0034952463 scopus 로고    scopus 로고
    • Efficient discovery of immune response targets by cyclical refinement of QSAR models of peptide binding
    • Brusic,V. et al. (2001) Efficient discovery of immune response targets by cyclical refinement of QSAR models of peptide binding. J Mol. Graph Model., 19, 405-411.
    • (2001) J Mol. Graph Model. , vol.19 , pp. 405-411
    • Brusic, V.1
  • 10
    • 0035989339 scopus 로고    scopus 로고
    • Prediction of promiscuous peptides that bind HLA class I molecules
    • Brusic,V. et al. (2002) Prediction of promiscuous peptides that bind HLA class I molecules. Immunol. Cell Biol., 80, 280-285.
    • (2002) Immunol. Cell Biol. , vol.80 , pp. 280-285
    • Brusic, V.1
  • 11
    • 10744222046 scopus 로고    scopus 로고
    • Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee'artificial neural network approach
    • Buus,S. et al. (2003) Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee'artificial neural network approach. Tissue Antigens, 62, 378-384.
    • (2003) Tissue Antigens , vol.62 , pp. 378-384
    • Buus, S.1
  • 12
    • 0031669217 scopus 로고    scopus 로고
    • A geometric study of the amino acid sequence of class I HLA molecules
    • Cano,P. et al. (1998) A geometric study of the amino acid sequence of class I HLA molecules. Immunogenetics, 48, 324-334.
    • (1998) Immunogenetics , vol.48 , pp. 324-334
    • Cano, P.1
  • 13
    • 0029956865 scopus 로고    scopus 로고
    • A roadmap for HLA-A, HLA-B, and HLA-C peptide binding specificities
    • Chelvanayagam,G. (1996) A roadmap for HLA-A, HLA-B, and HLA-C peptide binding specificities. Immunogenetics, 45, 15-26.
    • (1996) Immunogenetics , vol.45 , pp. 15-26
    • Chelvanayagam, G.1
  • 14
    • 0030747677 scopus 로고    scopus 로고
    • Degenerate cytotoxic T cell epitopes from P. falciparum restricted by multiple HLA-A and HLA-B supertype alleles
    • Doolan,D.L. et al. (1997) Degenerate cytotoxic T cell epitopes from P. falciparum restricted by multiple HLA-A and HLA-B supertype alleles. Immunity, 7, 97-112.
    • (1997) Immunity , vol.7 , pp. 97-112
    • Doolan, D.L.1
  • 15
    • 0142174642 scopus 로고    scopus 로고
    • Prediction of MHC class I binding peptides, using SVMHC
    • Dönnes,P. and Elofsson,A. (2002) Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics, 3, 25-32.
    • (2002) BMC Bioinformatics , vol.3 , pp. 25-32
    • Dönnes, P.1    Elofsson, A.2
  • 16
    • 1642407844 scopus 로고    scopus 로고
    • Identifying human MHC supertypes using bioinformatics methods
    • Doytchinova,I.A. et al. (2004) Identifying human MHC supertypes using bioinformatics methods. J. Immunol., 172, 4314-4323.
    • (2004) J. Immunol. , vol.172 , pp. 4314-4323
    • Doytchinova, I.A.1
  • 17
    • 0025855156 scopus 로고
    • Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules
    • Falk,K. et al. (1991) Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature, 351, 290-296.
    • (1991) Nature , vol.351 , pp. 290-296
    • Falk, K.1
  • 18
    • 0017480535 scopus 로고
    • A recursive partitioning decision rule for non-parametric classification
    • Friedman,J.H. (1977) A recursive partitioning decision rule for non-parametric classification. IEEE Trans. Comput., 26, 404-408.
    • (1977) IEEE Trans. Comput. , vol.26 , pp. 404-408
    • Friedman, J.H.1
  • 19
    • 0031576987 scopus 로고    scopus 로고
    • Two complementary methods for predicting peptides binding major histocompatibility complex molecules
    • Gulukota,K. et al. (1997) Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J. Mol. Biol., 267, 1258-1267.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1258-1267
    • Gulukota, K.1
  • 20
    • 0027937713 scopus 로고
    • Precise prediction of MHC class II-peptide interaction based on peptide side chain scanning
    • Hammer,J. et al. (1994) Precise prediction of MHC class II-peptide interaction based on peptide side chain scanning. J. Exp. Med., 180, 2353-2358.
    • (1994) J. Exp. Med. , vol.180 , pp. 2353-2358
    • Hammer, J.1
  • 21
    • 0027461057 scopus 로고
    • Contrasting roles of interallelic recombination at the HLA-A and HLA-B loci
    • Hughes,A.L. et al. (1993) Contrasting roles of interallelic recombination at the HLA-A and HLA-B loci. Genetics, (133), 669-680.
    • (1993) Genetics , Issue.133 , pp. 669-680
    • Hughes, A.L.1
  • 22
    • 0028913497 scopus 로고
    • Self peptides bound by HLA class I molecules are derived from highly conserved regions of a set of evolutionarily conserved proteins
    • Hughes,A.L. and Hughes,M.K. (1995) Self peptides bound by HLA class I molecules are derived from highly conserved regions of a set of evolutionarily conserved proteins. Immunogenetics, 41, 257-262.
    • (1995) Immunogenetics , vol.41 , pp. 257-262
    • Hughes, A.L.1    Hughes, M.K.2
  • 24
    • 0345863935 scopus 로고    scopus 로고
    • The KEGG resource for deciphering the genome
    • Kanehisa,M. et al. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, 277-280.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 277-280
    • Kanehisa, M.1
  • 25
    • 0027450353 scopus 로고
    • The molecular descent of the major histocompatibility complex
    • Klein,J. et al. (1993) The molecular descent of the major histocompatibility complex. Annu. Rev. Immunol., 11, 269-295.
    • (1993) Annu. Rev. Immunol. , vol.11 , pp. 269-295
    • Klein, J.1
  • 26
    • 0025257111 scopus 로고
    • Evolution of class-I MHC genes and proteins: From natural selection to thymic selection
    • Lawlor,D.A. et al. (1990) Evolution of class-I MHC genes and proteins: from natural selection to thymic selection. Annu. Rev. Inummol., 8, 23-63.
    • (1990) Annu. Rev. Inummol. , vol.8 , pp. 23-63
    • Lawlor, D.A.1
  • 27
    • 2342561929 scopus 로고    scopus 로고
    • Definition of supertypes for HLA molecules using clustering of specificity matrices
    • Lund,O. et al. (2004) Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics, 55, 797-810.
    • (2004) Immunogenetics , vol.55 , pp. 797-810
    • Lund, O.1
  • 28
    • 0032387825 scopus 로고    scopus 로고
    • Predicting peptides that bind to MHC molecules using supervised learning of hidden markov models
    • Mamitsuka,H. (1998) Predicting peptides that bind to MHC molecules using supervised learning of hidden markov models. Proteins., 33, 460-474.
    • (1998) Proteins. , vol.33 , pp. 460-474
    • Mamitsuka, H.1
  • 29
    • 0033224450 scopus 로고    scopus 로고
    • Taxonomic hierarchy of HLA class I allele sequences
    • McKenzie,L.M. et al. (1999) Taxonomic hierarchy of HLA class I allele sequences. Genes Immun., 1, 120-129.
    • (1999) Genes Immun. , vol.1 , pp. 120-129
    • McKenzie, L.M.1
  • 30
    • 2442499729 scopus 로고    scopus 로고
    • Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach
    • Nielsen,M. et al. (2004) Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics, 20, 1388-1397.
    • (2004) Bioinformatics , vol.20 , pp. 1388-1397
    • Nielsen, M.1
  • 31
    • 0001213826 scopus 로고
    • Nature of polymorphism in HLA-A, -B, and -C molecules
    • Parham,P. et al. (1988) Nature of polymorphism in HLA-A, -B, and -C molecules. Proc. Natl Acad. Sci. USA., 85, 4005-4009.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 4005-4009
    • Parham, P.1
  • 32
    • 0028052724 scopus 로고
    • Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual side chain scanning
    • Parker,K. et al. (1994) Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual side chain scanning. J. Immunol., 152, 163-175.
    • (1994) J. Immunol. , vol.152 , pp. 163-175
    • Parker, K.1
  • 33
    • 0141617555 scopus 로고    scopus 로고
    • Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules
    • Peters,B. et al. (2003) Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics, 19, 1765-1772.
    • (2003) Bioinformatics , vol.19 , pp. 1765-1772
    • Peters, B.1
  • 34
    • 0002442571 scopus 로고
    • Discovering rules by induction from large collections of examples
    • Michie,D. (ed.), Edinburgh, UK, Edinburgh University Press
    • Quinlan,J.R. (1979) Discovering rules by induction from large collections of examples. In Michie,D. (ed.), Expert Systems in the Micro Electronic Age. Edinburgh, UK, Edinburgh University Press, pp. 168-201.
    • (1979) Expert Systems in the Micro Electronic Age , pp. 168-201
    • Quinlan, J.R.1
  • 36
    • 0028985984 scopus 로고
    • MHC ligands and peptide motifs: 1st listing
    • Rammensee,H.G. et al. (1995) MHC ligands and peptide motifs: 1st listing. Immunogenetics, 41, 178-228.
    • (1995) Immunogenetics , vol.41 , pp. 178-228
    • Rammensee, H.G.1
  • 37
    • 0033388725 scopus 로고    scopus 로고
    • SYFPEITHI: Database for MHC ligands and peptide motifs
    • Rammensee,H.G. et al. (1999) SYFPEITHI: Database for MHC ligands and peptide motifs. Immunogenetics, 50, 213-219.
    • (1999) Immunogenetics , vol.50 , pp. 213-219
    • Rammensee, H.G.1
  • 38
    • 0036727207 scopus 로고    scopus 로고
    • Prediction of MHC class I binding peptides using profile motifs
    • Reche,P.A. et al. (2002) Prediction of MHC class I binding peptides using profile motifs. Hum. Immunol., 63, 701-709.
    • (2002) Hum. Immunol. , vol.63 , pp. 701-709
    • Reche, P.A.1
  • 39
    • 18244389000 scopus 로고    scopus 로고
    • Peptide binding at class I MHC scored with linear functions and support vector machines
    • Riedesel,H. et al. (2004) Peptide binding at class I MHC scored with linear functions and support vector machines. Gen. Inform., 15, 198-212.
    • (2004) Gen. Inform. , vol.15 , pp. 198-212
    • Riedesel, H.1
  • 40
    • 0027304399 scopus 로고
    • Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules
    • Ruppert,J. et al. (1993) Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules. Cell, 74, 929-937.
    • (1993) Cell , vol.74 , pp. 929-937
    • Ruppert, J.1
  • 41
    • 0037216895 scopus 로고    scopus 로고
    • Population of the HLA ligand database
    • Sathiamurthy,M. et al. (2003) Population of the HLA ligand database. Tissue Antigens, 61, 12-19.
    • (2003) Tissue Antigens , vol.61 , pp. 12-19
    • Sathiamurthy, M.1
  • 42
    • 0036081083 scopus 로고    scopus 로고
    • FIMM, a database of functional molecular immunology update 2002
    • Schönbach,C. et al. (2002) FIMM, a database of functional molecular immunology update 2002. Nucleic Acids Res., 30, 226-229.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 226-229
    • Schönbach, C.1
  • 43
    • 0035009714 scopus 로고    scopus 로고
    • Relating amino acid sequence to phenotype: Analysis of peptide-binding data
    • Segal,A. et al. (2001) Relating amino acid sequence to phenotype: analysis of peptide-binding data. Biometrics, 57, 632-642.
    • (2001) Biometrics , vol.57 , pp. 632-642
    • Segal, A.1
  • 44
    • 0033388724 scopus 로고    scopus 로고
    • Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism
    • Sette,A. et al. (1999) Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics, 50, 201-212.
    • (1999) Immunogenetics , vol.50 , pp. 201-212
    • Sette, A.1
  • 45
    • 0037363891 scopus 로고    scopus 로고
    • Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution
    • Sette,A. et al. (2003) Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution. Immunogenetics, 54, 830-841.
    • (2003) Immunogenetics , vol.54 , pp. 830-841
    • Sette, A.1
  • 46
    • 4544297611 scopus 로고    scopus 로고
    • Prediction of class IT-cell eptiopes: Evidence of presence of immunological hot spots inside antigens
    • Srinivasan,K.N. et al. (2004) Prediction of class IT-cell eptiopes: evidence of presence of immunological hot spots inside antigens. Bioinformatics, 20 (suppl.1), i297-i302.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Srinivasan, K.N.1
  • 47
    • 0033021020 scopus 로고    scopus 로고
    • Generation of tissue-specific and promiscuous HLA ligand database using DNA microarrays and virtual HLA class II matrices
    • Sturniolo,T. et al. (1999) Generation of tissue-specific and promiscuous HLA ligand database using DNA microarrays and virtual HLA class II matrices. Nat. Biotechnol., 17, 555-561.
    • (1999) Nat. Biotechnol. , vol.17 , pp. 555-561
    • Sturniolo, T.1
  • 48
    • 0029005514 scopus 로고
    • Decrypting the structure of MHC-I restricted CTL epitopes with complex peptide libraries
    • Udaka,K. et al. (1995) Decrypting the structure of MHC-I restricted CTL epitopes with complex peptide libraries. J Exp. Med., 181, 2097-2108.
    • (1995) J Exp. Med. , vol.181 , pp. 2097-2108
    • Udaka, K.1
  • 49
    • 0033866228 scopus 로고    scopus 로고
    • An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries
    • Udaka,K. et al. (2000) An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries. Immunogenetics, 51, 816-828.
    • (2000) Immunogenetics , vol.51 , pp. 816-828
    • Udaka, K.1
  • 50
    • 0037111212 scopus 로고    scopus 로고
    • Empirical evaluation of a dynamic experiment design method for prediction of MHC class I-binding peptides
    • Udaka,K. et al. (2002) Empirical evaluation of a dynamic experiment design method for prediction of MHC class I-binding peptides. J. Immunol., 169, 5744-5753.
    • (2002) J. Immunol. , vol.169 , pp. 5744-5753
    • Udaka, K.1
  • 51
    • 1442275185 scopus 로고    scopus 로고
    • Learning when training data are costly: The effect of class distribution on tree induction
    • Weiss,G.M. and Provost,F. (2003) Learning when training data are costly: the effect of class distribution on tree induction. J. Artif. Intell. Res., 19, 315-354.
    • (2003) J. Artif. Intell. Res. , vol.19 , pp. 315-354
    • Weiss, G.M.1    Provost, F.2
  • 52
    • 0036042580 scopus 로고    scopus 로고
    • Methods for prediction of peptide binding to MHC molecules: A comparative study
    • Yu,K. et al. (2002) Methods for prediction of peptide binding to MHC molecules: A comparative study. Mol. Med., 8, 137-148.
    • (2002) Mol. Med. , vol.8 , pp. 137-148
    • Yu, K.1
  • 53
    • 0032483463 scopus 로고    scopus 로고
    • Structural principles that govern the peptide-binding motifs of class I MHC molecules
    • Zhang,C. et al. (1998) Structural principles that govern the peptide-binding motifs of class I MHC molecules. J. Mol. Biol., 281, 929-947.
    • (1998) J. Mol. Biol. , vol.281 , pp. 929-947
    • Zhang, C.1


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