메뉴 건너뛰기




Volumn 130, Issue 3, 2010, Pages 309-318

Major histocompatibility complex class i binding predictions as a tool in epitope discovery

Author keywords

Cytotoxic T lymphocytes; Epitope prediction; Human leucocyte antigen; Major histocompatibility complex class I; Major histocompatibility complex peptide binding

Indexed keywords

EPITOPE; HLA A ANTIGEN; HLA B ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1;

EID: 77953496862     PISSN: 00192805     EISSN: 13652567     Source Type: Journal    
DOI: 10.1111/j.1365-2567.2010.03300.x     Document Type: Review
Times cited : (108)

References (101)
  • 1
    • 34247891741 scopus 로고    scopus 로고
    • More than one reason to rethink the use of peptides in vaccine design
    • Purcell AW, McCluskey J, Rossjohn J. More than one reason to rethink the use of peptides in vaccine design. Nat Rev Drug Discov 2007 6 : 404 414.
    • (2007) Nat Rev Drug Discov , vol.6 , pp. 404-414
    • Purcell, A.W.1    McCluskey, J.2    Rossjohn, J.3
  • 3
    • 70449338115 scopus 로고    scopus 로고
    • Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands
    • Juncker AS, Larsen MV, Weinhold N, Nielsen M, Brunak S, Lund O. Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands. PLoS ONE 2009 4 : e7448.
    • (2009) PLoS ONE , vol.4 , pp. 7448
    • Juncker, A.S.1    Larsen, M.V.2    Weinhold, N.3    Nielsen, M.4    Brunak, S.5    Lund, O.6
  • 5
    • 18644375874 scopus 로고    scopus 로고
    • + T cells by exogenous cell-associated antigens
    • + T cells by exogenous cell-associated antigens. Immunity 2002 17 : 211 220.
    • (2002) Immunity , vol.17 , pp. 211-220
    • Jung, S.1    Unutmaz, D.2    Wong, P.3
  • 7
    • 34548736008 scopus 로고    scopus 로고
    • Recent advances in antigen processing and presentation
    • Jensen PE. Recent advances in antigen processing and presentation. Nat Immunol 2007 8 : 1041 1048.
    • (2007) Nat Immunol , vol.8 , pp. 1041-1048
    • Jensen, P.E.1
  • 8
    • 3242771511 scopus 로고    scopus 로고
    • Generation of major histocompatibility complex class i antigens: Functional interplay between proteasomes and TPPII
    • Kloetzel PM. Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII. Nat Immunol 2004 5 : 661 669.
    • (2004) Nat Immunol , vol.5 , pp. 661-669
    • Kloetzel, P.M.1
  • 9
    • 70349437285 scopus 로고    scopus 로고
    • The peptide-loading complex - Antigen translocation and MHC class i loading
    • Schölz C, Tampé R. The peptide-loading complex - antigen translocation and MHC class I loading. Biol Chem 2009 390 : 783 794.
    • (2009) Biol Chem , vol.390 , pp. 783-794
    • Schölz, C.1    Tampé, R.2
  • 11
    • 0346727127 scopus 로고    scopus 로고
    • Protein degradation and protection against misfolded or damaged proteins
    • Goldberg AL. Protein degradation and protection against misfolded or damaged proteins. Nature 2003 426 : 895 899.
    • (2003) Nature , vol.426 , pp. 895-899
    • Goldberg, A.L.1
  • 12
    • 68749106118 scopus 로고    scopus 로고
    • New roles of flavoproteins in molecular cell biology: An unexpected role for quinone reductases as regulators of proteasomal degradation
    • Sollner S, Macheroux P. New roles of flavoproteins in molecular cell biology: an unexpected role for quinone reductases as regulators of proteasomal degradation. FEBS J 2009 276 : 4313 4324.
    • (2009) FEBS J , vol.276 , pp. 4313-4324
    • Sollner, S.1    MacHeroux, P.2
  • 14
    • 33646587050 scopus 로고    scopus 로고
    • The intracellular antigen transport machinery TAP in adaptive immunity and virus escape mechanisms
    • Schölz C, Tampé R. The intracellular antigen transport machinery TAP in adaptive immunity and virus escape mechanisms. J Bioenerg Biomembr 2005 37 : 509 515.
    • (2005) J Bioenerg Biomembr , vol.37 , pp. 509-515
    • Schölz, C.1    Tampé, R.2
  • 15
    • 26844477450 scopus 로고    scopus 로고
    • Critical role for the tapasin-docking site of TAP2 in the functional integrity of the MHC class I-peptide-loading complex
    • Leonhardt RM, Keusekotten K, Bekpen C, Knittler MR. Critical role for the tapasin-docking site of TAP2 in the functional integrity of the MHC class I-peptide-loading complex. J Immunol 2005 175 : 5104 5114.
    • (2005) J Immunol , vol.175 , pp. 5104-5114
    • Leonhardt, R.M.1    Keusekotten, K.2    Bekpen, C.3    Knittler, M.R.4
  • 16
    • 0032005348 scopus 로고    scopus 로고
    • Soluble tapasin restores MHC class i expression and function in the tapasin-negative cell line.220
    • Lehner PJ, Surman MJ, Cresswell P. Soluble tapasin restores MHC class I expression and function in the tapasin-negative cell line.220. Immunity 1998 8 : 221 231.
    • (1998) Immunity , vol.8 , pp. 221-231
    • Lehner, P.J.1    Surman, M.J.2    Cresswell, P.3
  • 17
    • 0033046472 scopus 로고    scopus 로고
    • Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses
    • Yewdell JW, Bennink JR. Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu Rev Immunol 1999 17 : 51 88.
    • (1999) Annu Rev Immunol , vol.17 , pp. 51-88
    • Yewdell, J.W.1    Bennink, J.R.2
  • 18
    • 9644289334 scopus 로고    scopus 로고
    • The proteasome and MHC class i antigen processing
    • Kloetzel PM. The proteasome and MHC class I antigen processing. Biochim Biophys Acta 2004 1695 : 225 233.
    • (2004) Biochim Biophys Acta , vol.1695 , pp. 225-233
    • Kloetzel, P.M.1
  • 19
    • 77949352951 scopus 로고    scopus 로고
    • The MHC motif viewer: A visualization tool for MHC binding motifs
    • Chapter 18, Unit 18.17.
    • Rapin N, Hoof I, Lund O, Nielsen M. The MHC motif viewer: a visualization tool for MHC binding motifs. Curr Protoc Immunol 2010 Chapter 18, Unit 18.17.
    • Curr Protoc Immunol 2010
    • Rapin, N.1    Hoof, I.2    Lund, O.3    Nielsen, M.4
  • 20
    • 36949010425 scopus 로고    scopus 로고
    • Modelling the human immune system by combining bioinformatics and systems biology approaches
    • Rapin N, Kesmir C, Frankild S, Nielsen M, Lundegaard C, Brunak S, Lund O. Modelling the human immune system by combining bioinformatics and systems biology approaches. J Biol Phys 2006 32 : 335 353.
    • (2006) J Biol Phys , vol.32 , pp. 335-353
    • Rapin, N.1    Kesmir, C.2    Frankild, S.3    Nielsen, M.4    Lundegaard, C.5    Brunak, S.6    Lund, O.7
  • 21
  • 22
    • 0023115557 scopus 로고
    • The relation between major histocompatibility complex (MHC) restriction and the capacity of Ia to bind immunogenic peptides
    • Buus S, Sette A, Colon SM, Miles C, Grey HM. The relation between major histocompatibility complex (MHC) restriction and the capacity of Ia to bind immunogenic peptides. Science 1987 235 : 1353 1358.
    • (1987) Science , vol.235 , pp. 1353-1358
    • Buus, S.1    Sette, A.2    Colon, S.M.3    Miles, C.4    Grey, H.M.5
  • 23
    • 0028842070 scopus 로고
    • Several HLA alleles share overlapping peptide specificities
    • Sidney J, del Guercio MF, Southwood S et al. Several HLA alleles share overlapping peptide specificities. J Immunol 1995 154 : 247 259.
    • (1995) J Immunol , vol.154 , pp. 247-259
    • Sidney, J.1    Del Guercio, M.F.2    Southwood, S.3
  • 24
    • 44649087768 scopus 로고    scopus 로고
    • The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods
    • Guan P, Doytchinova IA, Flower DR. The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods. Methods Mol Biol 2007 409 : 143 154.
    • (2007) Methods Mol Biol , vol.409 , pp. 143-154
    • Guan, P.1    Doytchinova, I.A.2    Flower, D.R.3
  • 25
    • 44649137451 scopus 로고    scopus 로고
    • Definition of MHC supertypes through clustering of MHC peptide-binding repertoires
    • Reche PA, Reinherz EL. Definition of MHC supertypes through clustering of MHC peptide-binding repertoires. Methods Mol Biol 2007 409 : 163 173.
    • (2007) Methods Mol Biol , vol.409 , pp. 163-173
    • Reche, P.A.1    Reinherz, E.L.2
  • 26
    • 1642407844 scopus 로고    scopus 로고
    • Identifiying human MHC supertypes using bioinformatic methods
    • Doytchinova IA, Guan P, Flower DR. Identifiying human MHC supertypes using bioinformatic methods. J Immunol 2004 172 : 4314 4323.
    • (2004) J Immunol , vol.172 , pp. 4314-4323
    • Doytchinova, I.A.1    Guan, P.2    Flower, D.R.3
  • 27
    • 33846662153 scopus 로고    scopus 로고
    • Identifying HLA supertypes by learning distance functions
    • Hertz T, Yanover C. Identifying HLA supertypes by learning distance functions. Bioinformatics 2007 23 : e148 55.
    • (2007) Bioinformatics , vol.23 , pp. 148-55
    • Hertz, T.1    Yanover, C.2
  • 28
    • 2342561929 scopus 로고    scopus 로고
    • Definition of supertypes for HLA molecules using clustering of specificity matrices
    • Lund O, Nielsen M, Kesmir C et al. Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics 2004 55 : 797 810.
    • (2004) Immunogenetics , vol.55 , pp. 797-810
    • Lund, O.1    Nielsen, M.2    Kesmir, C.3
  • 29
    • 39649122106 scopus 로고    scopus 로고
    • HLA class i supertypes: A revised and updated classification
    • Sidney J, Peters B, Frahm N, Brander C, Sette A. HLA class I supertypes: a revised and updated classification. BMC Immunol 2008 9 : 1471 2172.
    • (2008) BMC Immunol , vol.9 , pp. 1471-2172
    • Sidney, J.1    Peters, B.2    Frahm, N.3    Brander, C.4    Sette, A.5
  • 31
    • 58149336996 scopus 로고    scopus 로고
    • Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype
    • Hillen N, Mester G, Lemmel C et al. Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype. Eur J Immunol 2008 38 : 2993 3003.
    • (2008) Eur J Immunol , vol.38 , pp. 2993-3003
    • Hillen, N.1    Mester, G.2    Lemmel, C.3
  • 32
    • 33745584371 scopus 로고    scopus 로고
    • A community resource benchmarking predictions of peptide binding to MHC-I molecules
    • Peters B, Bui HH, Frankild S et al. A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol 2006 2 : e65.
    • (2006) PLoS Comput Biol , vol.2 , pp. 65
    • Peters, B.1    Bui, H.H.2    Frankild, S.3
  • 36
    • 0035993241 scopus 로고    scopus 로고
    • Establishment of a quantitative ELISA capable of determining peptide-MHC class i interaction
    • Sylvester-Hvid C, Kristensen N, Blicher T et al. Establishment of a quantitative ELISA capable of determining peptide-MHC class I interaction. Tissue Antigens 2002 59 : 251 258.
    • (2002) Tissue Antigens , vol.59 , pp. 251-258
    • Sylvester-Hvid, C.1    Kristensen, N.2    Blicher, T.3
  • 37
    • 61849124792 scopus 로고    scopus 로고
    • Peptide binding to HLA class i molecules: Homogenous, high-throughput screening, and affinity assays
    • Harndahl M, Justesen S, Lamberth K, Røder G, Nielsen M, Buus S. Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays. J Biomol Screen 2009 14 : 173 180.
    • (2009) J Biomol Screen , vol.14 , pp. 173-180
    • Harndahl, M.1    Justesen, S.2    Lamberth, K.3    Røder, G.4    Nielsen, M.5    Buus, S.6
  • 38
    • 0028915529 scopus 로고
    • Receptor-ligand interactions measured by an improved spun column chromatography technique. A high efficiency and high throughput size separation method
    • Buus S, Stryhn A, Winther K, Kirkby N, Pedersen LO. Receptor-ligand interactions measured by an improved spun column chromatography technique. A high efficiency and high throughput size separation method. Biochim Biophys Acta 1995 1243 : 453 460.
    • (1995) Biochim Biophys Acta , vol.1243 , pp. 453-460
    • Buus, S.1    Stryhn, A.2    Winther, K.3    Kirkby, N.4    Pedersen, L.O.5
  • 39
    • 0027205314 scopus 로고
    • Direct detection of major histocompatibility complex class i binding to antigenic peptides using surface plasmon resonance. Peptide immobilization and characterization of binding specificity
    • Khilko SN, Corr M, Boyd LF, Lees A, Inman JK, Margulies DH. Direct detection of major histocompatibility complex class I binding to antigenic peptides using surface plasmon resonance. Peptide immobilization and characterization of binding specificity. J Biol Chem 1993 268 : 15425 15434.
    • (1993) J Biol Chem , vol.268 , pp. 15425-15434
    • Khilko, S.N.1    Corr, M.2    Boyd, L.F.3    Lees, A.4    Inman, J.K.5    Margulies, D.H.6
  • 40
    • 67650270386 scopus 로고    scopus 로고
    • Identification of human MHC class i binding peptides using the iTOPIA-epitope discovery system
    • Wulf M, Hoehn P, Trinder P. Identification of human MHC class I binding peptides using the iTOPIA-epitope discovery system. Methods Mol Biol 2009 524 : 361 367.
    • (2009) Methods Mol Biol , vol.524 , pp. 361-367
    • Wulf, M.1    Hoehn, P.2    Trinder, P.3
  • 42
    • 77953528024 scopus 로고    scopus 로고
    • Pillars article: Association of class i major histocompatibility heavy and light chains induced by viral peptides. Nature 1989. 340: 443-448
    • Townsend A, Ohlén C, Bastin J, Ljunggren HG, Foster L, Kärre K. Pillars article: association of class I major histocompatibility heavy and light chains induced by viral peptides. Nature 1989. 340: 443-448. J Immunol 2007 179 : 4301 4306.
    • (2007) J Immunol , vol.179 , pp. 4301-4306
    • Townsend, A.1    Ohlén, C.2    Bastin, J.3    Ljunggren, H.G.4    Foster, L.5    Kärre, K.6
  • 43
    • 0027955071 scopus 로고
    • A quantitative assay to measure the interaction between immunogenic peptides and purified class i major histocompatibility complex molecules
    • Olsen AC, Pedersen LO, Hansen AS, Nissen MH, Olsen M, Hansen PR, Holm A, Buus S. A quantitative assay to measure the interaction between immunogenic peptides and purified class I major histocompatibility complex molecules. Eur J Immunol 1994 24 : 385 392.
    • (1994) Eur J Immunol , vol.24 , pp. 385-392
    • Olsen, A.C.1    Pedersen, L.O.2    Hansen, A.S.3    Nissen, M.H.4    Olsen, M.5    Hansen, P.R.6    Holm, A.7    Buus, S.8
  • 44
    • 20944447214 scopus 로고    scopus 로고
    • The immune epitope database and analysis resource: From vision to blueprint
    • Peters B, Sidney J, Bourne P et al. The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol 2005 3 : e91.
    • (2005) PLoS Biol , vol.3 , pp. 91
    • Peters, B.1    Sidney, J.2    Bourne, P.3
  • 45
    • 70449416038 scopus 로고    scopus 로고
    • Prediction of MHC-peptide binding: A systematic and comprehensive overview
    • Lafuente EM, Reche PA. Prediction of MHC-peptide binding: a systematic and comprehensive overview. Curr Pharm Des 2009 15 : 3209 3220.
    • (2009) Curr Pharm des , vol.15 , pp. 3209-3220
    • Lafuente, E.M.1    Reche, P.A.2
  • 46
    • 77949494386 scopus 로고    scopus 로고
    • Limitations of Ab initio predictions of peptide binding to MHC class II molecules
    • Zhang H, Wang P, Papangelopoulos N., et al. Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PLoS One 2010 5 : e9272.
    • (2010) PLoS One , vol.5 , pp. 9272
    • Zhang, H.1    Wang, P.2    Papangelopoulos, N.3
  • 47
    • 0025155682 scopus 로고
    • Cellular peptide composition governed by major histocompatibility complex class i molecules
    • Falk K, Rotzschke O, Rammensee HG. Cellular peptide composition governed by major histocompatibility complex class I molecules. Nature 1990 348 : 248 251.
    • (1990) Nature , vol.348 , pp. 248-251
    • Falk, K.1    Rotzschke, O.2    Rammensee, H.G.3
  • 48
    • 0025855156 scopus 로고
    • Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules
    • Falk K, Rötzschke O, Stevanović S, Jung G, Rammensee HG. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 1991 351 : 290 296.
    • (1991) Nature , vol.351 , pp. 290-296
    • Falk, K.1    Rötzschke, O.2    Stevanović, S.3    Jung, G.4    Rammensee, H.G.5
  • 51
    • 0028052724 scopus 로고
    • Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains
    • Parker KC, Bednarek MA, Coligan JE. Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol 1994 152 : 163 175.
    • (1994) J Immunol , vol.152 , pp. 163-175
    • Parker, K.C.1    Bednarek, M.A.2    Coligan, J.E.3
  • 52
    • 9444240941 scopus 로고    scopus 로고
    • Peptide binding specificity of major histocompatibility complex class i resolved into an array of apparently independent subspecificities: Quantitation by peptide libraries and improved prediction of binding
    • Stryhn A, Pedersen LO, Romme T, Holm CB, Holm A, Buus S. Peptide binding specificity of major histocompatibility complex class I resolved into an array of apparently independent subspecificities: quantitation by peptide libraries and improved prediction of binding. Eur J Immunol 1996 26 : 1911 1918.
    • (1996) Eur J Immunol , vol.26 , pp. 1911-1918
    • Stryhn, A.1    Pedersen, L.O.2    Romme, T.3    Holm, C.B.4    Holm, A.5    Buus, S.6
  • 53
    • 0033866228 scopus 로고    scopus 로고
    • An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries
    • Udaka K, Wiesmüller KH, Kienle S et al. An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries. Immunogenetics 2000 51 : 816 828.
    • (2000) Immunogenetics , vol.51 , pp. 816-828
    • Udaka, K.1    Wiesmüller, K.H.2    Kienle, S.3
  • 55
    • 0036727207 scopus 로고    scopus 로고
    • Prediction of MHC class i binding peptides using profile motifs
    • Reche PA, Glutting JP, Reinherz EL. Prediction of MHC class I binding peptides using profile motifs. Hum Immunol 2002 63 : 701 709.
    • (2002) Hum Immunol , vol.63 , pp. 701-709
    • Reche, P.A.1    Glutting, J.P.2    Reinherz, E.L.3
  • 57
    • 0032387825 scopus 로고    scopus 로고
    • Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models
    • Mamitsuka H. Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models. Proteins 1998 33 : 460 474.
    • (1998) Proteins , vol.33 , pp. 460-474
    • Mamitsuka, H.1
  • 58
    • 21344466799 scopus 로고    scopus 로고
    • Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications
    • Bui HH, Sidney J, Peters B et al. Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 2005 57 : 304 314.
    • (2005) Immunogenetics , vol.57 , pp. 304-314
    • Bui, H.H.1    Sidney, J.2    Peters, B.3
  • 59
    • 25444476693 scopus 로고    scopus 로고
    • Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
    • Peters B, Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 2005 6 : 132.
    • (2005) BMC Bioinformatics , vol.6 , pp. 132
    • Peters, B.1    Sette, A.2
  • 60
    • 0141617555 scopus 로고    scopus 로고
    • Examining the independent binding assumption for binding of peptide epitopes to MHC-1 molecules
    • Peters B, Tong WW, Sidney J, Sette A, Weng ZP. Examining the independent binding assumption for binding of peptide epitopes to MHC-1 molecules. Bioinformatics 2003 19 : 1765 1772.
    • (2003) Bioinformatics , vol.19 , pp. 1765-1772
    • Peters, B.1    Tong, W.W.2    Sidney, J.3    Sette, A.4    Weng, Z.P.5
  • 62
    • 10744222046 scopus 로고    scopus 로고
    • Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach
    • Buus S, Lauemoller SL, Worning P et al. Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 2003 62 : 378 384.
    • (2003) Tissue Antigens , vol.62 , pp. 378-384
    • Buus, S.1    Lauemoller, S.L.2    Worning, P.3
  • 64
    • 0142174642 scopus 로고    scopus 로고
    • Prediction of MHC class i binding peptides, using SVMHC
    • Donnes P, Elofsson A. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 2002 3 : 25.
    • (2002) BMC Bioinformatics , vol.3 , pp. 25
    • Donnes, P.1    Elofsson, A.2
  • 65
    • 33847710294 scopus 로고    scopus 로고
    • Prediction of supertype-specific HLA class i binding peptides using support vector machines
    • Zhang GL, Bozic I, Kwoh CK, August JT, Brusic V. Prediction of supertype-specific HLA class I binding peptides using support vector machines. J Immunol Methods 2007 320 : 143 154.
    • (2007) J Immunol Methods , vol.320 , pp. 143-154
    • Zhang, G.L.1    Bozic, I.2    Kwoh, C.K.3    August, J.T.4    Brusic, V.5
  • 66
    • 0142148183 scopus 로고    scopus 로고
    • Application of support vector machines for T-cell epitopes prediction
    • Zhao Y, Pinilla C, Valmori D, Martin R, Simon R. Application of support vector machines for T-cell epitopes prediction. Bioinformatics 2003 19 : 1978.
    • (2003) Bioinformatics , vol.19 , pp. 1978
    • Zhao, Y.1    Pinilla, C.2    Valmori, D.3    Martin, R.4    Simon, R.5
  • 67
    • 3843052528 scopus 로고    scopus 로고
    • Prediction of CTL epitopes using QM, SVM and ANN techniques
    • Bhasin M, Raghava GP. Prediction of CTL epitopes using QM, SVM and ANN techniques. Vaccine 2004 22 : 3195 3204.
    • (2004) Vaccine , vol.22 , pp. 3195-3204
    • Bhasin, M.1    Raghava, G.P.2
  • 68
    • 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
    • Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M. 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 2008 36 : W509 12.
    • (2008) Nucleic Acids Res , vol.36 , pp. 509-12
    • Lundegaard, C.1    Lamberth, K.2    Harndahl, M.3    Buus, S.4    Lund, O.5    Nielsen, M.6
  • 69
    • 42549105195 scopus 로고    scopus 로고
    • Evaluation of MHC class i peptide binding prediction servers: Applications for vaccine research
    • Lin HH, Ray S, Tongchusak S, Reinherz EL, Brusic V. Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol 2008 9 : 8.
    • (2008) BMC Immunol , vol.9 , pp. 8
    • Lin, H.H.1    Ray, S.2    Tongchusak, S.3    Reinherz, E.L.4    Brusic, V.5
  • 70
    • 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
    • Lundegaard C, Lund O, Nielsen M. 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 2008 24 : 1397 1398.
    • (2008) Bioinformatics , vol.24 , pp. 1397-1398
    • Lundegaard, C.1    Lund, O.2    Nielsen, M.3
  • 71
    • 34548794906 scopus 로고    scopus 로고
    • Extensive HLA class i allele promiscuity among viral CTL epitopes
    • Frahm N, Yusim K, Suscovich TJ et al. Extensive HLA class I allele promiscuity among viral CTL epitopes. Eur J Immunol 2007 37 : 2419 2433.
    • (2007) Eur J Immunol , vol.37 , pp. 2419-2433
    • Frahm, N.1    Yusim, K.2    Suscovich, T.J.3
  • 74
    • 34547653712 scopus 로고    scopus 로고
    • Leveraging information across HLA alleles/supertypes improves epitope prediction
    • Heckerman D, Kadie C, Listgarten J. Leveraging information across HLA alleles/supertypes improves epitope prediction. J Comput Biol 2007 14 : 736 746.
    • (2007) J Comput Biol , vol.14 , pp. 736-746
    • Heckerman, D.1    Kadie, C.2    Listgarten, J.3
  • 75
    • 38849139819 scopus 로고    scopus 로고
    • Efficient peptide-MHC-I binding prediction for alleles with few known binders
    • Jacob L, Vert JP. Efficient peptide-MHC-I binding prediction for alleles with few known binders. Bioinformatics 2008 24 : 358 366.
    • (2008) Bioinformatics , vol.24 , pp. 358-366
    • Jacob, L.1    Vert, J.P.2
  • 76
    • 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
    • Nielsen M, Lundegaard C, Blicher T et al. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS ONE 2007 2 : e796.
    • (2007) PLoS ONE , vol.2 , pp. 796
    • Nielsen, M.1    Lundegaard, C.2    Blicher, T.3
  • 77
    • 33845790971 scopus 로고    scopus 로고
    • A modular concept of HLA for comprehensive peptide binding prediction
    • DeLuca DS, Khattab B, Blasczyk R. A modular concept of HLA for comprehensive peptide binding prediction. Immunogenetics 2007 59 : 25 35.
    • (2007) Immunogenetics , vol.59 , pp. 25-35
    • Deluca, D.S.1    Khattab, B.2    Blasczyk, R.3
  • 78
    • 65549131038 scopus 로고    scopus 로고
    • The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: Application to MHC-peptide binding
    • Zhang H, Lund O, Nielsen M. The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. Bioinformatics 2009 25 : 1293 1299.
    • (2009) Bioinformatics , vol.25 , pp. 1293-1299
    • Zhang, H.1    Lund, O.2    Nielsen, M.3
  • 79
    • 58049217445 scopus 로고    scopus 로고
    • Pan-specific MHC class i predictors: A benchmark of HLA class i pan-specific prediction methods
    • Zhang H, Lundegaard C, Nielsen M. Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. Bioinformatics 2009 25 : 83 9.
    • (2009) Bioinformatics , vol.25 , pp. 83-9
    • Zhang, H.1    Lundegaard, C.2    Nielsen, M.3
  • 80
    • 17844385106 scopus 로고    scopus 로고
    • The role of the proteasome in generating cytotoxic T-cell epitopes: Insights obtained from improved predictions of proteasomal cleavage
    • Nielsen M, Lundegaard C, Lund O, Keşmir C. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 2005 57 : 33 41.
    • (2005) Immunogenetics , vol.57 , pp. 33-41
    • Nielsen, M.1    Lundegaard, C.2    Lund, O.3    Keşmir, C.4
  • 81
    • 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, Endert PMV, Holzhutter HG. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol 2003 171 : 1741 1749.
    • (2003) J Immunol , vol.171 , pp. 1741-1749
    • Peters, B.1    Bulik, S.2    Tampe, R.3    Endert, P.M.V.4    Holzhutter, H.G.5
  • 83
    • 20844434026 scopus 로고    scopus 로고
    • Modeling the MHC class i pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class i binding
    • Tenzer S, Peters B, Bulik S et al. Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci 2005 62 : 1025 1037.
    • (2005) Cell Mol Life Sci , vol.62 , pp. 1025-1037
    • Tenzer, S.1    Peters, B.2    Bulik, S.3
  • 84
    • 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
    • Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M. 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 2005 35 : 2295 2303.
    • (2005) Eur J Immunol , vol.35 , 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
  • 86
    • 33947265265 scopus 로고    scopus 로고
    • CTL epitopes for influenza A including the H5N1 bird flu; Genome-, pathogen-, and HLA-wide screening
    • Wang M, Lamberth K, Harndahl M et al. CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening. Vaccine 2007 25 : 2823 2831.
    • (2007) Vaccine , vol.25 , pp. 2823-2831
    • Wang, M.1    Lamberth, K.2    Harndahl, M.3
  • 87
    • 58149165030 scopus 로고    scopus 로고
    • A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines
    • Toussaint NC, Dönnes P, Kohlbacher O. A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines. PLoS Comput Biol 2008 4 : e1000246.
    • (2008) PLoS Comput Biol , vol.4 , pp. 1000246
    • Toussaint, N.C.1    Dönnes, P.2    Kohlbacher, O.3
  • 88
    • 67849111553 scopus 로고    scopus 로고
    • OptiTope - A web server for the selection of an optimal set of peptides for epitope-based vaccines
    • Toussaint NC, Kohlbacher O. OptiTope - a web server for the selection of an optimal set of peptides for epitope-based vaccines. Nucleic Acids Res 2009 37 : W617 22.
    • (2009) Nucleic Acids Res , vol.37 , pp. 617-22
    • Toussaint, N.C.1    Kohlbacher, O.2
  • 89
    • 44449117504 scopus 로고    scopus 로고
    • Broadly immunogenic HLA class i supertype-restricted elite CTL epitopes recognized in a diverse population infected with different HIV-1 subtypes
    • Perez CL, Larsen MV, Gustafsson R et al. Broadly immunogenic HLA class I supertype-restricted elite CTL epitopes recognized in a diverse population infected with different HIV-1 subtypes. J Immunol 2008 180 : 5092 5100.
    • (2008) J Immunol , vol.180 , pp. 5092-5100
    • Perez, C.L.1    Larsen, M.V.2    Gustafsson, R.3
  • 90
    • 0034046248 scopus 로고    scopus 로고
    • Poor correspondence between predicted and experimental binding of peptides to class i MHC molecules
    • Andersen MH, Tan L, Søndergaard I, Zeuthen J, Elliott T, Haurum JS. Poor correspondence between predicted and experimental binding of peptides to class I MHC molecules. Tissue Antigens 2000 55 : 519 531.
    • (2000) Tissue Antigens , vol.55 , pp. 519-531
    • Andersen, M.H.1    Tan, L.2    Søndergaard, I.3    Zeuthen, J.4    Elliott, T.5    Haurum, J.S.6
  • 91
    • 0027399839 scopus 로고
    • A method to quantify binding of unlabeled peptides to class i MHC molecules and detect their allele specificity
    • Elvin J, Potter C, Elliott T, Cerundolo V, Townsend A. A method to quantify binding of unlabeled peptides to class I MHC molecules and detect their allele specificity. J Immunol Methods 1993 158 : 161 171.
    • (1993) J Immunol Methods , vol.158 , pp. 161-171
    • Elvin, J.1    Potter, C.2    Elliott, T.3    Cerundolo, V.4    Townsend, A.5
  • 92
    • 70350457586 scopus 로고    scopus 로고
    • In silico methods for predicting T-cell epitopes: Dr Jekyll or Mr Hyde?
    • Gowthaman U, Agrewala JN. In silico methods for predicting T-cell epitopes: Dr Jekyll or Mr Hyde? Expert Rev Proteomics 2009 6 : 527 537.
    • (2009) Expert Rev Proteomics , vol.6 , pp. 527-537
    • Gowthaman, U.1    Agrewala, J.N.2
  • 95
    • 43549119527 scopus 로고    scopus 로고
    • Mapping of cytotoxic T lymphocytes epitopes in E7 antigen of human papillomavirus type 11
    • Xu Y, Zhu KJ, Chen XZ, Zhao KJ, Lu ZM, Cheng H. Mapping of cytotoxic T lymphocytes epitopes in E7 antigen of human papillomavirus type 11. Arch Dermatol Res 2008 300 : 235 242.
    • (2008) Arch Dermatol Res , vol.300 , pp. 235-242
    • Xu, Y.1    Zhu, K.J.2    Chen, X.Z.3    Zhao, K.J.4    Lu, Z.M.5    Cheng, H.6
  • 96
    • 0028295047 scopus 로고
    • Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins
    • Kast WM, Brandt RM, Sidney J, Drijfhout JW, Kubo RT, Grey HM, Melief CJ, Sette A. Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins. J Immunol 1994 152 : 3904 3912.
    • (1994) J Immunol , vol.152 , pp. 3904-3912
    • Kast, W.M.1    Brandt, R.M.2    Sidney, J.3    Drijfhout, J.W.4    Kubo, R.T.5    Grey, H.M.6    Melief, C.J.7    Sette, A.8
  • 97
    • 0027304399 scopus 로고
    • Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules
    • Ruppert J, Sidney J, Celis E, Kubo RT, Grey HM, Sette A. Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules. Cell 1993 74 : 929 937.
    • (1993) Cell , vol.74 , pp. 929-937
    • Ruppert, J.1    Sidney, J.2    Celis, E.3    Kubo, R.T.4    Grey, H.M.5    Sette, A.6
  • 98
    • 53849146699 scopus 로고    scopus 로고
    • MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination
    • Tang ST, Wang M, Lamberth K, Harndahl M, Dziegiel MH, Claesson MH, Buus S, Lund O. MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination. Arch Virol 2008 153 : 1833 1844.
    • (2008) Arch Virol , vol.153 , pp. 1833-1844
    • Tang, S.T.1    Wang, M.2    Lamberth, K.3    Harndahl, M.4    Dziegiel, M.H.5    Claesson, M.H.6    Buus, S.7    Lund, O.8
  • 100
    • 7944223046 scopus 로고    scopus 로고
    • Computational methods for prediction of T-cell epitopes - A framework for modelling, testing, and applications
    • Brusic V, Bajic VB, Petrovsky N. Computational methods for prediction of T-cell epitopes - a framework for modelling, testing, and applications. Methods 2004 34 : 436 443.
    • (2004) Methods , vol.34 , pp. 436-443
    • Brusic, V.1    Bajic, V.B.2    Petrovsky, N.3
  • 101
    • 57649174707 scopus 로고    scopus 로고
    • Evaluation of MHC-II peptide binding prediction servers: Applications for vaccine research
    • Lin HH, Zhang GL, Tongchusak S, Reinherz EL, Brusic V. Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics 2008 9 (Suppl. 12 S22.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 12 , pp. 22
    • Lin, H.H.1    Zhang, G.L.2    Tongchusak, S.3    Reinherz, E.L.4    Brusic, V.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.