메뉴 건너뛰기




Volumn 66, Issue 7-8, 2014, Pages 449-456

NetTepi: An integrated method for the prediction of T cell epitopes

Author keywords

Cytotoxic T lymphocyte; MHC binding specificity; MHC class I; Peptide immunogenicity; Peptide MHC binding stability; T cell epitope

Indexed keywords

EPITOPE; T LYMPHOCYTE RECEPTOR;

EID: 84904250653     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-014-0779-0     Document Type: Article
Times cited : (53)

References (37)
  • 1
    • 0028675323 scopus 로고
    • Development of high potency universal DR-restricted helper epitopes by modification of high affinity DR-blocking peptides
    • Alexander J, Sidney J, Southwood S et al (1994) Development of high potency universal DR-restricted helper epitopes by modification of high affinity DR-blocking peptides. Immunity 1:751-761
    • (1994) Immunity , vol.1 , pp. 751-761
    • Alexander, J.1    Sidney, J.2    Southwood, S.3
  • 3
    • 84861173090 scopus 로고    scopus 로고
    • Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire
    • doi:10.1371/journal.pcbi.1002412
    • Calis JJ, de Boer RJ, Keşmir C (2012) Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PLoS Comput Biol 8:e1002412. doi:10.1371/journal.pcbi.1002412
    • (2012) PLoS Comput Biol , vol.8
    • Calis, J.J.1    De Boer, R.J.2    Keşmir, C.3
  • 4
    • 84887277467 scopus 로고    scopus 로고
    • Properties of MHC class I presented peptides that enhance immunogenicity
    • doi:10.1371/journal.pcbi.1003266
    • Calis JJA, Maybeno M, Greenbaum JA et al (2013) Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol 9:e1003266. doi:10.1371/journal.pcbi.1003266
    • (2013) PLoS Comput Biol , vol.9
    • Calis, J.J.A.1    Maybeno, M.2    Greenbaum, J.A.3
  • 5
    • 0025855156 scopus 로고
    • Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules
    • Falk K, Rötzschke O, Stevanović S et al (1991) Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 351:290-296. doi:10.1038/351290a0 (Pubitemid 21896578)
    • (1991) Nature , vol.351 , Issue.6324 , pp. 290-296
    • Falk, K.1    Rotzschke, O.2    Stevanovic, S.3    Jung, G.4    Rammensee, H.-G.5
  • 6
    • 0028077007 scopus 로고
    • Efficient MHC class I-peptide binding is required but does not ensure MHC class I-restricted immunogenicity
    • DOI 10.1016/0161-5890(94)90155-4
    • Feltkamp MC, Vierboom MP, Kast WM, Melief CJ (1994) Efficient MHC class I-peptide binding is required but does not ensure MHC class I-restricted immunogenicity. Mol Immunol 31:1391-1401 (Pubitemid 24381796)
    • (1994) Molecular Immunology , vol.31 , Issue.18 , pp. 1391-1401
    • Feltkamp, M.C.W.1    Vierboom, M.P.M.2    Kast, M.3    Melief, C.J.M.4
  • 7
    • 46649086131 scopus 로고    scopus 로고
    • Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire
    • doi:10.1371/journal.pone.0001831
    • Frankild S, de Boer RJ, Lund O et al (2008) Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire. PLoS ONE 3:e1831. doi:10.1371/journal.pone.0001831
    • (2008) PLoS ONE , vol.3
    • Frankild, S.1    De Boer, R.J.2    Lund, O.3
  • 8
    • 84862152481 scopus 로고    scopus 로고
    • Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity
    • doi:10.1002/eji.201141774
    • Harndahl M, Rasmussen M, Roder G et al (2012) Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity. Eur J Immunol 42:1405-1416. doi:10.1002/eji.201141774
    • (2012) Eur J Immunol , vol.42 , pp. 1405-1416
    • Harndahl, M.1    Rasmussen, M.2    Roder, G.3
  • 9
    • 0034097041 scopus 로고    scopus 로고
    • + T cell effector mechanisms in resistance to infection
    • DOI 10.1146/annurev.immunol.18.1.275
    • Harty JT, Tvinnereim AR, White DW (2000) CD8+ T cell effector mechanisms in resistance to infection. Annu Rev Immunol 18:275-308. doi:10.1146/annurev. immunol.18.1.275 (Pubitemid 30365382)
    • (2000) Annual Review of Immunology , vol.18 , pp. 275-308
    • Harty, J.T.1    Tvinnereim, A.R.2    White, D.W.3
  • 10
    • 59449094834 scopus 로고    scopus 로고
    • NetMHCpan, a method for MHC class I binding prediction beyond humans
    • doi:10.1007/s00251-008-0341-z
    • Hoof I, Peters B, Sidney J et al (2009) NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61:1-13. doi:10.1007/s00251-008-0341-z
    • (2009) Immunogenetics , vol.61 , pp. 1-13
    • Hoof, I.1    Peters, B.2    Sidney, J.3
  • 12
    • 84889637320 scopus 로고    scopus 로고
    • NetMHCstab - Predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery
    • doi:10.1111/imm.12160
    • Jørgensen KW, Rasmussen M, Buus S, Nielsen M (2014) NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery. Immunology 141:18-26. doi:10.1111/imm.12160
    • (2014) Immunology , vol.141 , pp. 18-26
    • Jørgensen, K.W.1    Rasmussen, M.2    Buus, S.3    Nielsen, M.4
  • 13
    • 84857362309 scopus 로고    scopus 로고
    • NetMHCcons: A consensus method for the major histocompatibility complex class I predictions
    • doi:10.1007/s00251-011-0579-8
    • Karosiene E, Lundegaard C, Lund O, Nielsen M (2012) NetMHCcons: a consensus method for the major histocompatibility complex class I predictions. Immunogenetics 64:177-186. doi:10.1007/s00251-011-0579-8
    • (2012) Immunogenetics , vol.64 , pp. 177-186
    • Karosiene, E.1    Lundegaard, C.2    Lund, O.3    Nielsen, M.4
  • 15
    • 84864424747 scopus 로고    scopus 로고
    • Immune epitope database analysis resource
    • doi:10.1093/nar/gks438
    • Kim Y, Ponomarenko J, Zhu Z et al (2012) Immune epitope database analysis resource. Nucleic Acids Res 40:W525-W530. doi:10.1093/nar/gks438
    • (2012) Nucleic Acids Res , vol.40
    • Kim, Y.1    Ponomarenko, J.2    Zhu, Z.3
  • 16
    • 38049169092 scopus 로고    scopus 로고
    • Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction
    • doi:10.1186/1471-2105-8-424
    • Larsen MV, Lundegaard C, Lamberth K et al (2007) Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinforma 8:424. doi:10.1186/1471-2105-8-424
    • (2007) BMC Bioinforma , vol.8 , pp. 424
    • Larsen, M.V.1    Lundegaard, C.2    Lamberth, K.3
  • 17
    • 23844528191 scopus 로고    scopus 로고
    • An integrative approach to CTL epitope prediction: A combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions
    • DOI 10.1002/eji.200425811
    • Larsen MV, Lundegaard C, Lamberth K et al (2005) An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol 35:2295-2303. doi:10.1002/eji.200425811 (Pubitemid 41179750)
    • (2005) European Journal of Immunology , vol.35 , Issue.8 , pp. 2295-2303
    • Larsen, M.V.1    Lundegaard, C.2    Lamberth, K.3    Buus, S.4    Brunak, S.5    Lund, O.6    Nielsen, M.7
  • 19
    • 48449106045 scopus 로고    scopus 로고
    • NetMHC-3.0: Accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11
    • doi:10.1093/nar/gkn202
    • Lundegaard C, Lamberth K, Harndahl M et al (2008a) NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.Nucleic Acids Res 36:W509-W512. doi:10.1093/nar/gkn202
    • (2008) Nucleic Acids Res , vol.36
    • Lundegaard, C.1    Lamberth, K.2    Harndahl, M.3
  • 20
    • 77953496862 scopus 로고    scopus 로고
    • Major histocompatibility complex class I binding predictions as a tool in epitope discovery
    • doi:10.1111/j.1365-2567.2010.03300.x
    • Lundegaard C, Lund O, Buus S, Nielsen M (2010) Major histocompatibility complex class I binding predictions as a tool in epitope discovery. Immunology 130:309-318. doi:10.1111/j.1365-2567.2010.03300.x
    • (2010) Immunology , vol.130 , pp. 309-318
    • Lundegaard, C.1    Lund, O.2    Buus, S.3    Nielsen, M.4
  • 21
    • 83155164579 scopus 로고    scopus 로고
    • Predictions versus highthroughput experiments in T-cell epitope discovery: Competition or synergy?
    • doi:10.1586/erv.11.160
    • Lundegaard C, Lund O, Nielsen M (2012) Predictions versus highthroughput experiments in T-cell epitope discovery: competition or synergy? Expert Rev Vaccines 11:43-54. doi:10.1586/erv.11.160
    • (2012) Expert Rev Vaccines , vol.11 , pp. 43-54
    • Lundegaard, C.1    Lund, O.2    Nielsen, M.3
  • 22
    • 44349146151 scopus 로고    scopus 로고
    • Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers
    • DOI 10.1093/bioinformatics/btn128
    • Lundegaard C, Lund O, Nielsen M (2008b) Accurate approximation method for prediction of class IMHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioinformatics 24:1397-1398. doi:10.1093/bioinformatics/btn128 (Pubitemid 351737147)
    • (2008) Bioinformatics , vol.24 , Issue.11 , pp. 1397-1398
    • Lundegaard, C.1    Lund, O.2    Nielsen, M.3
  • 23
    • 39549084433 scopus 로고    scopus 로고
    • NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence
    • doi:10.1371/journal.pone.0000796
    • Nielsen M, Lundegaard C, Blicher T et al (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. doi:10.1371/journal.pone.0000796
    • (2007) PLoS ONE , vol.2
    • Nielsen, M.1    Lundegaard, C.2    Blicher, T.3
  • 24
    • 17844385106 scopus 로고    scopus 로고
    • The role of the proteasome in generating cytotoxic T-cell epitopes: Insights obtained from improved predictions of proteasomal cleavage
    • DOI 10.1007/s00251-005-0781-7
    • Nielsen M, Lundegaard C, Lund O, Keşmir C (2005) The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 57:33-41. doi:10.1007/s00251-005-0781-7 (Pubitemid 40591245)
    • (2005) Immunogenetics , vol.57 , Issue.1-2 , pp. 33-41
    • Nielsen, M.1    Lundegaard, C.2    Lund, O.3    Kesmir, C.4
  • 26
    • 0041589474 scopus 로고    scopus 로고
    • Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors
    • Peters B, Bulik S, Tampe R et al (2003) Identifying HC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol 171:1741-1749 (Pubitemid 36966457)
    • (2003) Journal of Immunology , vol.171 , Issue.4 , pp. 1741-1749
    • Peters, B.1    Bulik, S.2    Tampe, R.3    Van Endert, P.M.4    Holzhutter, H.-G.5
  • 27
    • 25444476693 scopus 로고    scopus 로고
    • Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
    • doi:10.1186/1471-2105-6-132
    • Peters B, Sette A (2005) Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinforma 6:132. doi:10.1186/1471-2105-6-132
    • (2005) BMC Bioinforma , vol.6 , pp. 132
    • Peters, B.1    Sette, A.2
  • 29
    • 33646181088 scopus 로고    scopus 로고
    • How TCRs bind MHCs, peptides, and coreceptors
    • doi:10.1146/annurev.immunol.23.021704.115658
    • Rudolph MG, Stanfield RL, Wilson IA (2006) How TCRs bind MHCs, peptides, and coreceptors. Annu Rev Immunol 24:419-466. doi:10.1146/annurev.immunol.23. 021704.115658
    • (2006) Annu Rev Immunol , vol.24 , pp. 419-466
    • Rudolph, M.G.1    Stanfield, R.L.2    Wilson, I.A.3
  • 30
    • 77953149616 scopus 로고    scopus 로고
    • NetCTLpan: Pan-specific MHC class I pathway epitope predictions
    • doi:10.1007/s00251-010-0441-4
    • Stranzl T, Larsen MV, Lundegaard C, Nielsen M (2010) NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics 62:357-368. doi:10.1007/s00251-010-0441-4
    • (2010) Immunogenetics , vol.62 , pp. 357-368
    • Stranzl, T.1    Larsen, M.V.2    Lundegaard, C.3    Nielsen, M.4
  • 32
    • 81055124275 scopus 로고    scopus 로고
    • POPISK: T-cell reactivity prediction using support vector machines and string kernels
    • doi:10.1186/1471-2105-12-446
    • Tung C-W, Ziehm M, Kämper A et al (2011) POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinforma 12:446. doi:10.1186/1471-2105-12-446
    • (2011) BMC Bioinforma , vol.12 , pp. 446
    • Tung, C.-W.1    Ziehm, M.2    Kämper, A.3
  • 33
    • 27744607218 scopus 로고    scopus 로고
    • The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation
    • doi:10.1084/jem.20050864
    • Tynan FE, Elhassen D, Purcell AW et al (2005) The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation. J Exp Med 202:1249-1260. doi:10.1084/jem.20050864
    • (2005) J Exp Med , vol.202 , pp. 1249-1260
    • Tynan, F.E.1    Elhassen, D.2    Purcell, A.W.3
  • 34
    • 75549084463 scopus 로고    scopus 로고
    • The immune epitope database 2.0
    • doi:10.1093/nar/gkp1004
    • Vita R, Zarebski L, Greenbaum JA et al (2010) The immune epitope database 2.0. Nucleic Acids Res 38:D854-D862. doi:10.1093/nar/gkp1004
    • (2010) Nucleic Acids Res , vol.38
    • Vita, R.1    Zarebski, L.2    Greenbaum, J.A.3
  • 35
    • 84878446213 scopus 로고    scopus 로고
    • Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells
    • doi:10.1073/pnas.1305227110
    • Weiskopf D, Angelo MA, de Azeredo EL et al (2013) Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells. Proc Natl Acad Sci U S A 110:E2046-E2053. doi:10.1073/pnas. 1305227110
    • (2013) Proc Natl Acad Sci U S A , vol.110
    • Weiskopf, D.1    Angelo, M.A.2    De Azeredo, E.L.3
  • 36
    • 0033046472 scopus 로고    scopus 로고
    • Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses
    • doi:10.1146/annurev.immunol.17.1.51
    • Yewdell JW, Bennink JR (1999) Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu Rev Immunol 17:51-88. doi:10.1146/annurev.immunol.17.1.51
    • (1999) Annu Rev Immunol , vol.17 , pp. 51-88
    • Yewdell, J.W.1    Bennink, J.R.2
  • 37
    • 65549131038 scopus 로고    scopus 로고
    • The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: Application to MHC-peptide binding
    • doi:10.1093/bioinformatics/btp137
    • Zhang H, Lund O, Nielsen M (2009) The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. Bioinformatics 25:1293-1299. doi:10.1093/bioinformatics/btp137
    • (2009) Bioinformatics , vol.25 , pp. 1293-1299
    • Zhang, H.1    Lund, O.2    Nielsen, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.