메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

POPISK: T-cell reactivity prediction using support vector machines and string kernels

Author keywords

[No Author keywords available]

Indexed keywords

10-FOLD CROSS-VALIDATION; ACCURATE PREDICTION; ANTIGEN PROCESSING; LARGE-SCALE ANALYSIS; PEPTIDE SEQUENCES; PHYSICOCHEMICAL PROPERTY; REACTIVITY PREDICTION; STRUCTURAL FEATURE;

EID: 81055124275     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-446     Document Type: Article
Times cited : (63)

References (75)
  • 1
    • 58149165030 scopus 로고    scopus 로고
    • A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines
    • 10.1371/journal.pcbi.1000246, 2588662, 19112482
    • Toussaint NC, Donnes P, Kohlbacher O. A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines. PLoS Comput Biol 2008, 4(12):e1000246. 10.1371/journal.pcbi.1000246, 2588662, 19112482.
    • (2008) PLoS Comput Biol , vol.4 , Issue.12
    • Toussaint, N.C.1    Donnes, P.2    Kohlbacher, O.3
  • 2
    • 67849111553 scopus 로고    scopus 로고
    • OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines
    • Web Server
    • 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 Web Server):W617-622.
    • (2009) Nucleic Acids Res , Issue.37
    • Toussaint, N.C.1    Kohlbacher, O.2
  • 3
    • 33748763304 scopus 로고    scopus 로고
    • Virus-epitope vaccine design: informatic matching the HLA-I polymorphism to the virus genome
    • 10.1016/j.molimm.2006.06.003, 16930710
    • Vider-Shalit T, Raffaeli S, Louzoun Y. Virus-epitope vaccine design: informatic matching the HLA-I polymorphism to the virus genome. Mol Immunol 2007, 44(6):1253-1261. 10.1016/j.molimm.2006.06.003, 16930710.
    • (2007) Mol Immunol , vol.44 , Issue.6 , pp. 1253-1261
    • Vider-Shalit, T.1    Raffaeli, S.2    Louzoun, Y.3
  • 4
    • 34250635170 scopus 로고    scopus 로고
    • Methods and protocols for prediction of immunogenic epitopes
    • Tong JC, Tan TW, Ranganathan S. Methods and protocols for prediction of immunogenic epitopes. Brief Bioinform 2007, 8(2):96-108.
    • (2007) Brief Bioinform , vol.8 , Issue.2 , pp. 96-108
    • Tong, J.C.1    Tan, T.W.2    Ranganathan, S.3
  • 5
    • 36949034073 scopus 로고    scopus 로고
    • Modeling the adaptive immune system: predictions and simulations
    • 10.1093/bioinformatics/btm471, 18045832
    • Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M. Modeling the adaptive immune system: predictions and simulations. Bioinformatics 2007, 23(24):3265-3275. 10.1093/bioinformatics/btm471, 18045832.
    • (2007) Bioinformatics , vol.23 , Issue.24 , pp. 3265-3275
    • Lundegaard, C.1    Lund, O.2    Kesmir, C.3    Brunak, S.4    Nielsen, M.5
  • 6
    • 84888277859 scopus 로고    scopus 로고
    • Towards in silico design of epitope-based vaccines
    • Toussaint NC, Kohlbacher O. Towards in silico design of epitope-based vaccines. 2009,
    • (2009)
    • Toussaint, N.C.1    Kohlbacher, O.2
  • 7
    • 0035074032 scopus 로고    scopus 로고
    • PAProC: a prediction algorithm for proteasomal cleavages available on the WWW
    • 10.1007/s002510100300, 11345595
    • Nussbaum AK, Kuttler C, Hadeler KP, Rammensee HG, Schild H. PAProC: a prediction algorithm for proteasomal cleavages available on the WWW. Immunogenetics 2001, 53(2):87-94. 10.1007/s002510100300, 11345595.
    • (2001) Immunogenetics , vol.53 , Issue.2 , pp. 87-94
    • Nussbaum, A.K.1    Kuttler, C.2    Hadeler, K.P.3    Rammensee, H.G.4    Schild, H.5
  • 8
    • 0036096708 scopus 로고    scopus 로고
    • Prediction of proteasome cleavage motifs by neural networks
    • 10.1093/protein/15.4.287, 11983929
    • Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S. Prediction of proteasome cleavage motifs by neural networks. Protein Eng 2002, 15(4):287-296. 10.1093/protein/15.4.287, 11983929.
    • (2002) Protein Eng , vol.15 , Issue.4 , pp. 287-296
    • Kesmir, C.1    Nussbaum, A.K.2    Schild, H.3    Detours, V.4    Brunak, S.5
  • 9
    • 23144433033 scopus 로고    scopus 로고
    • Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences
    • Web Server
    • Bhasin M, Raghava GP. Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences. Nucleic Acids Res 2005, (33 Web Server):W202-207.
    • (2005) Nucleic Acids Res , Issue.33
    • Bhasin, M.1    Raghava, G.P.2
  • 10
    • 1342268087 scopus 로고    scopus 로고
    • Analysis and prediction of affinity of TAP binding peptides using cascade SVM
    • 10.1110/ps.03373104, 2286721, 14978300
    • Bhasin M, Raghava GP. Analysis and prediction of affinity of TAP binding peptides using cascade SVM. Protein Sci 2004, 13(3):596-607. 10.1110/ps.03373104, 2286721, 14978300.
    • (2004) Protein Sci , vol.13 , Issue.3 , pp. 596-607
    • Bhasin, M.1    Raghava, G.P.2
  • 11
    • 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, Van Endert PM, Holzhutter HG. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol 2003, 171(4):1741-1749.
    • (2003) J Immunol , 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
  • 12
    • 0033388725 scopus 로고    scopus 로고
    • SYFPEITHI: database for MHC ligands and peptide motifs
    • 10.1007/s002510050595, 10602881
    • Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S. SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 1999, 50(3-4):213-219. 10.1007/s002510050595, 10602881.
    • (1999) Immunogenetics , vol.50 , Issue.3-4 , pp. 213-219
    • Rammensee, H.1    Bachmann, J.2    Emmerich, N.P.3    Bachor, O.A.4    Stevanovic, S.5
  • 13
    • 44649153892 scopus 로고    scopus 로고
    • SYFPEITHI: database for searching and T-cell epitope prediction
    • 10.1007/978-1-60327-118-9_5, 18449993
    • Schuler MM, Nastke MD, Stevanovikc S. SYFPEITHI: database for searching and T-cell epitope prediction. Methods Mol Biol 2007, 409:75-93. 10.1007/978-1-60327-118-9_5, 18449993.
    • (2007) Methods Mol Biol , vol.409 , pp. 75-93
    • Schuler, M.M.1    Nastke, M.D.2    Stevanovikc, S.3
  • 14
    • 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. Journal of Immunology 1994, 152(1):163-175.
    • (1994) Journal of Immunology , vol.152 , Issue.1 , pp. 163-175
    • Parker, K.C.1    Bednarek, M.A.2    Coligan, J.E.3
  • 15
    • 0142174642 scopus 로고    scopus 로고
    • Prediction of MHC class I binding peptides, using SVMHC
    • 10.1186/1471-2105-3-25, 129981, 12225620
    • Donnes P, Elofsson A. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 2002, 3:25. 10.1186/1471-2105-3-25, 129981, 12225620.
    • (2002) BMC Bioinformatics , vol.3 , pp. 25
    • Donnes, P.1    Elofsson, A.2
  • 16
    • 33747839161 scopus 로고    scopus 로고
    • SVMHC: a server for prediction of MHC-binding peptides
    • Web Server
    • Donnes P, Kohlbacher O. SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res 2006, (34 Web Server):W194-197.
    • (2006) Nucleic Acids Res , Issue.34
    • Donnes, P.1    Kohlbacher, O.2
  • 18
    • 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
    • 10.1371/journal.pone.0000796, 1949492, 17726526
    • Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Roder G, Peters B, Sette A, Lund O, 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(8):e796. 10.1371/journal.pone.0000796, 1949492, 17726526.
    • (2007) PLoS One , vol.2 , Issue.8
    • Nielsen, M.1    Lundegaard, C.2    Blicher, T.3    Lamberth, K.4    Harndahl, M.5    Justesen, S.6    Roder, G.7    Peters, B.8    Sette, A.9    Lund, O.10
  • 19
    • 38849139819 scopus 로고    scopus 로고
    • Efficient peptide-MHC-I binding prediction for alleles with few known binders
    • Bioinformatics (Oxford, England)
    • Jacob L, Vert JP. Efficient peptide-MHC-I binding prediction for alleles with few known binders. 2008, 24(3):358-366. Bioinformatics (Oxford, England).
    • (2008) , vol.24 , Issue.3 , pp. 358-366
    • Jacob, L.1    Vert, J.P.2
  • 20
    • 5444249860 scopus 로고    scopus 로고
    • Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles
    • Reche PA, Glutting JP, Zhang H, Reinherz EL. Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics 2004, 56(6):405-419.
    • (2004) Immunogenetics , vol.56 , Issue.6 , pp. 405-419
    • Reche, P.A.1    Glutting, J.P.2    Zhang, H.3    Reinherz, E.L.4
  • 21
    • 44649189266 scopus 로고    scopus 로고
    • Prediction of peptide-MHC binding using profiles
    • 10.1007/978-1-60327-118-9_13, 18450001
    • Reche PA, Reinherz EL. Prediction of peptide-MHC binding using profiles. Methods Mol Biol 2007, 409:185-200. 10.1007/978-1-60327-118-9_13, 18450001.
    • (2007) Methods Mol Biol , vol.409 , pp. 185-200
    • Reche, P.A.1    Reinherz, E.L.2
  • 22
    • 44649155161 scopus 로고    scopus 로고
    • In silico prediction of peptide-MHC binding affinity using SVRMHC
    • 10.1007/978-1-60327-118-9_20, 18450008
    • Liu W, Wan J, Meng X, Flower DR, Li T. In silico prediction of peptide-MHC binding affinity using SVRMHC. Methods Mol Biol 2007, 409:283-291. 10.1007/978-1-60327-118-9_20, 18450008.
    • (2007) Methods Mol Biol , vol.409 , pp. 283-291
    • Liu, W.1    Wan, J.2    Meng, X.3    Flower, D.R.4    Li, T.5
  • 23
    • 33750464517 scopus 로고    scopus 로고
    • SVRMHC prediction server for MHC-binding peptides
    • 10.1186/1471-2105-7-463, 1626489, 17059589
    • Wan J, Liu W, Xu Q, Ren Y, Flower DR, Li T. SVRMHC prediction server for MHC-binding peptides. BMC Bioinformatics 2006, 7:463. 10.1186/1471-2105-7-463, 1626489, 17059589.
    • (2006) BMC Bioinformatics , vol.7 , pp. 463
    • Wan, J.1    Liu, W.2    Xu, Q.3    Ren, Y.4    Flower, D.R.5    Li, T.6
  • 24
    • 33746352651 scopus 로고    scopus 로고
    • Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models
    • 10.1186/1471-2105-7-182, 1513606, 16579851
    • Liu W, Meng X, Xu Q, Flower DR, Li T. Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. BMC Bioinformatics 2006, 7:182. 10.1186/1471-2105-7-182, 1513606, 16579851.
    • (2006) BMC Bioinformatics , vol.7 , pp. 182
    • Liu, W.1    Meng, X.2    Xu, Q.3    Flower, D.R.4    Li, T.5
  • 25
    • 33747892659 scopus 로고    scopus 로고
    • DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations
    • 10.1093/bioinformatics/btl216, 16873467
    • Antes I, Siu SW, Lengauer T. DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. Bioinformatics 2006, 22(14):e16-24. 10.1093/bioinformatics/btl216, 16873467.
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Antes, I.1    Siu, S.W.2    Lengauer, T.3
  • 26
    • 23644443226 scopus 로고    scopus 로고
    • Integrated modeling of the major events in the MHC class I antigen processing pathway
    • 10.1110/ps.051352405, 2279325, 15987883
    • Donnes P, Kohlbacher O. Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Science 2005, 14(8):2132-2140. 10.1110/ps.051352405, 2279325, 15987883.
    • (2005) Protein Science , vol.14 , Issue.8 , pp. 2132-2140
    • Donnes, P.1    Kohlbacher, O.2
  • 27
    • 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
    • 10.1002/eji.200425811, 15997466
    • 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(8):2295-2303. 10.1002/eji.200425811, 15997466.
    • (2005) Eur J Immunol , 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
  • 29
    • 20844434026 scopus 로고    scopus 로고
    • Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding
    • 10.1007/s00018-005-4528-2, 15868101
    • Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, Holzhutter HG. 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(9):1025-1037. 10.1007/s00018-005-4528-2, 15868101.
    • (2005) Cell Mol Life Sci , vol.62 , Issue.9 , pp. 1025-1037
    • Tenzer, S.1    Peters, B.2    Bulik, S.3    Schoor, O.4    Lemmel, C.5    Schatz, M.M.6    Kloetzel, P.M.7    Rammensee, H.G.8    Schild, H.9    Holzhutter, H.G.10
  • 30
    • 0030744321 scopus 로고    scopus 로고
    • The ability of peptides to induce cytotoxic T cells in vitro does not strongly correlate with their affinity for the H-2Ld molecule: implications for vaccine design and immunotherapy
    • 10.1016/S0161-5890(97)00019-9, 9224969
    • Ochoa-Garay J, McKinney DM, Kochounian HH, McMillan M. The ability of peptides to induce cytotoxic T cells in vitro does not strongly correlate with their affinity for the H-2Ld molecule: implications for vaccine design and immunotherapy. Mol Immunol 1997, 34(3):273-281. 10.1016/S0161-5890(97)00019-9, 9224969.
    • (1997) Mol Immunol , vol.34 , Issue.3 , pp. 273-281
    • Ochoa-Garay, J.1    McKinney, D.M.2    Kochounian, H.H.3    McMillan, M.4
  • 31
    • 34249687092 scopus 로고    scopus 로고
    • POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties
    • Tung CW, Ho SY. POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties. Bioinformatics (Oxford, England) 2007, 23(8):942-949.
    • (2007) Bioinformatics (Oxford, England) , vol.23 , Issue.8 , pp. 942-949
    • Tung, C.W.1    Ho, S.Y.2
  • 32
    • 33646019589 scopus 로고    scopus 로고
    • Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses
    • Bihl F, Frahm N, Di Giammarino L, Sidney J, John M, Yusim K, Woodberry T, Sango K, Hewitt HS, Henry L, et al. Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses. Journal of Immunology 2006, 176(7):4094-4101.
    • (2006) Journal of Immunology , vol.176 , Issue.7 , pp. 4094-4101
    • Bihl, F.1    Frahm, N.2    Di Giammarino, L.3    Sidney, J.4    John, M.5    Yusim, K.6    Woodberry, T.7    Sango, K.8    Hewitt, H.S.9    Henry, L.10
  • 33
    • 0028077007 scopus 로고
    • Efficient MHC class I-peptide binding is required but does not ensure MHC class I-restricted immunogenicity
    • 10.1016/0161-5890(94)90155-4, 7823965
    • Feltkamp MC, Vierboom MP, Kast WM, Melief CJ. Efficient MHC class I-peptide binding is required but does not ensure MHC class I-restricted immunogenicity. Mol Immunol 1994, 31(18):1391-1401. 10.1016/0161-5890(94)90155-4, 7823965.
    • (1994) Mol Immunol , vol.31 , Issue.18 , pp. 1391-1401
    • Feltkamp, M.C.1    Vierboom, M.P.2    Kast, W.M.3    Melief, C.J.4
  • 35
    • 0036082615 scopus 로고    scopus 로고
    • Structural and thermodynamic correlates of T cell signaling
    • 10.1146/annurev.biophys.31.082901.134423, 11988465
    • Rudolph MG, Luz JG, Wilson IA. Structural and thermodynamic correlates of T cell signaling. Annu Rev Biophys Biomol Struct 2002, 31:121-149. 10.1146/annurev.biophys.31.082901.134423, 11988465.
    • (2002) Annu Rev Biophys Biomol Struct , vol.31 , pp. 121-149
    • Rudolph, M.G.1    Luz, J.G.2    Wilson, I.A.3
  • 36
    • 0026621224 scopus 로고
    • Atomic structure of a human MHC molecule presenting an influenza virus peptide
    • 10.1038/360367a0, 1448154
    • Silver ML, Guo HC, Strominger JL, Wiley DC. Atomic structure of a human MHC molecule presenting an influenza virus peptide. Nature 1992, 360(6402):367-369. 10.1038/360367a0, 1448154.
    • (1992) Nature , vol.360 , Issue.6402 , pp. 367-369
    • Silver, M.L.1    Guo, H.C.2    Strominger, J.L.3    Wiley, D.C.4
  • 37
    • 0038300653 scopus 로고    scopus 로고
    • A structural basis for immunodominant human T cell receptor recognition
    • 10.1038/ni942, 12796775
    • Stewart-Jones GB, McMichael AJ, Bell JI, Stuart DI, Jones EY. A structural basis for immunodominant human T cell receptor recognition. Nat Immunol 2003, 4(7):657-663. 10.1038/ni942, 12796775.
    • (2003) Nat Immunol , vol.4 , Issue.7 , pp. 657-663
    • Stewart-Jones, G.B.1    McMichael, A.J.2    Bell, J.I.3    Stuart, D.I.4    Jones, E.Y.5
  • 38
    • 0028105911 scopus 로고
    • Identification of T cell receptor recognition residues for a viral peptide presented by HLA B27
    • 10.1002/eji.1830241015, 7523137
    • Bowness P, Allen RL, McMichael AJ. Identification of T cell receptor recognition residues for a viral peptide presented by HLA B27. Eur J Immunol 1994, 24(10):2357-2363. 10.1002/eji.1830241015, 7523137.
    • (1994) Eur J Immunol , vol.24 , Issue.10 , pp. 2357-2363
    • Bowness, P.1    Allen, R.L.2    McMichael, A.J.3
  • 39
    • 60549100596 scopus 로고    scopus 로고
    • HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels
    • 10.1186/1742-4690-5-110, 2637298, 19055831
    • Boisvert S, Marchand M, Laviolette F, Corbeil J. HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels. Retrovirology 2008, 5:110. 10.1186/1742-4690-5-110, 2637298, 19055831.
    • (2008) Retrovirology , vol.5 , pp. 110
    • Boisvert, S.1    Marchand, M.2    Laviolette, F.3    Corbeil, J.4
  • 40
    • 47649130438 scopus 로고    scopus 로고
    • Predicting linear B-cell epitopes using string kernels
    • 10.1002/jmr.893, 2683948, 18496882
    • El-Manzalawy Y, Dobbs D, Honavar V. Predicting linear B-cell epitopes using string kernels. J Mol Recognit 2008, 21(4):243-255. 10.1002/jmr.893, 2683948, 18496882.
    • (2008) J Mol Recognit , vol.21 , Issue.4 , pp. 243-255
    • El-Manzalawy, Y.1    Dobbs, D.2    Honavar, V.3
  • 42
    • 46249106500 scopus 로고    scopus 로고
    • POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors
    • Sonnenburg S, Zien A, Philips P, Ratsch G. POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors. Bioinformatics (Oxford, England) 2008, 24(13):i6-14.
    • (2008) Bioinformatics (Oxford, England) , vol.24 , Issue.13
    • Sonnenburg, S.1    Zien, A.2    Philips, P.3    Ratsch, G.4
  • 43
    • 0031811850 scopus 로고    scopus 로고
    • MHCPEP, a database of MHC-binding peptides: update 1997
    • 10.1093/nar/26.1.368, 147255, 9399876
    • Brusic V, Rudy G, Harrison LC. MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res 1998, 26(1):368-371. 10.1093/nar/26.1.368, 147255, 9399876.
    • (1998) Nucleic Acids Res , vol.26 , Issue.1 , pp. 368-371
    • Brusic, V.1    Rudy, G.2    Harrison, L.C.3
  • 44
    • 20944447214 scopus 로고    scopus 로고
    • The immune epitope database and analysis resource: from vision to blueprint
    • 10.1371/journal.pbio.0030091, 1065705, 15760272
    • Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, et al. The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol 2005, 3(3):e91. 10.1371/journal.pbio.0030091, 1065705, 15760272.
    • (2005) PLoS Biol , vol.3 , Issue.3
    • Peters, B.1    Sidney, J.2    Bourne, P.3    Bui, H.H.4    Buus, S.5    Doh, G.6    Fleri, W.7    Kronenberg, M.8    Kubo, R.9    Lund, O.10
  • 46
    • 0033165928 scopus 로고    scopus 로고
    • Four A6-TCR/peptide/HLA-A2 structures that generate very different T cell signals are nearly identical
    • 10.1016/S1074-7613(00)80080-1, 10435578
    • Ding YH, Baker BM, Garboczi DN, Biddison WE, Wiley DC. Four A6-TCR/peptide/HLA-A2 structures that generate very different T cell signals are nearly identical. Immunity 1999, 11(1):45-56. 10.1016/S1074-7613(00)80080-1, 10435578.
    • (1999) Immunity , vol.11 , Issue.1 , pp. 45-56
    • Ding, Y.H.1    Baker, B.M.2    Garboczi, D.N.3    Biddison, W.E.4    Wiley, D.C.5
  • 47
    • 33745622868 scopus 로고    scopus 로고
    • Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments
    • Vacic V, Iakoucheva LM, Radivojac P. Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics (Oxford, England) 2006, 22(12):1536-1537.
    • (2006) Bioinformatics (Oxford, England) , vol.22 , Issue.12 , pp. 1536-1537
    • Vacic, V.1    Iakoucheva, L.M.2    Radivojac, P.3
  • 48
    • 77950352237 scopus 로고    scopus 로고
    • TEpredict: software for T-cell epitope prediction
    • Antonets DV, Maksiutov AZ. TEpredict: software for T-cell epitope prediction. Molekuliarnaia Biologiia 2010, 44(1):130-139.
    • (2010) Molekuliarnaia Biologiia , vol.44 , Issue.1 , pp. 130-139
    • Antonets, D.V.1    Maksiutov, A.Z.2
  • 49
    • 66249085541 scopus 로고    scopus 로고
    • Prediction of HLA-DQ8beta cell peptidome using a computational program and its relationship to autoreactive T cells
    • 10.1093/intimm/dxp039, 2686615, 19461125
    • Chang KY, Unanue ER. Prediction of HLA-DQ8beta cell peptidome using a computational program and its relationship to autoreactive T cells. International Immunology 2009, 21(6):705-713. 10.1093/intimm/dxp039, 2686615, 19461125.
    • (2009) International Immunology , vol.21 , Issue.6 , pp. 705-713
    • Chang, K.Y.1    Unanue, E.R.2
  • 50
    • 60549116507 scopus 로고    scopus 로고
    • A set of new amino acid descriptors applied in prediction of MHC class I binding peptides
    • 10.1016/j.ejmech.2008.06.011, 18662841
    • Liang G, Yang L, Chen Z, Mei H, Shu M, Li Z. A set of new amino acid descriptors applied in prediction of MHC class I binding peptides. Eur J Med Chem 2009, 44(3):1144-1154. 10.1016/j.ejmech.2008.06.011, 18662841.
    • (2009) Eur J Med Chem , vol.44 , Issue.3 , pp. 1144-1154
    • Liang, G.1    Yang, L.2    Chen, Z.3    Mei, H.4    Shu, M.5    Li, Z.6
  • 51
    • 77956357957 scopus 로고    scopus 로고
    • Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system
    • 10.1371/journal.pone.0009862, 2855701, 20419125
    • Rapin N, Lund O, Bernaschi M, Castiglione F. Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PLoS One 2010, 5(4):e9862. 10.1371/journal.pone.0009862, 2855701, 20419125.
    • (2010) PLoS One , vol.5 , Issue.4
    • Rapin, N.1    Lund, O.2    Bernaschi, M.3    Castiglione, F.4
  • 57
    • 0003500248 scopus 로고
    • C4.5: programs for machine learning
    • San Mateo, CA: Morgan Kaufmann
    • Quinlan JR. C4.5: programs for machine learning. 1993, San Mateo, CA: Morgan Kaufmann.
    • (1993)
    • Quinlan, J.R.1
  • 59
    • 70349593251 scopus 로고    scopus 로고
    • Using multidimensional patterns of amino acid attributes for QSAR analysis of peptides
    • 10.1007/s00726-008-0177-8, 18821054
    • Liang G, Yang L, Kang L, Mei H, Li Z. Using multidimensional patterns of amino acid attributes for QSAR analysis of peptides. Amino Acids 2009, 37(4):583-591. 10.1007/s00726-008-0177-8, 18821054.
    • (2009) Amino Acids , vol.37 , Issue.4 , pp. 583-591
    • Liang, G.1    Yang, L.2    Kang, L.3    Mei, H.4    Li, Z.5
  • 60
    • 67349182211 scopus 로고    scopus 로고
    • In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure-activity relationship approach
    • 10.1007/s00726-008-0116-8, 18575802
    • Tian F, Yang L, Lv F, Yang Q, Zhou P. In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure-activity relationship approach. Amino Acids 2009, 36(3):535-554. 10.1007/s00726-008-0116-8, 18575802.
    • (2009) Amino Acids , vol.36 , Issue.3 , pp. 535-554
    • Tian, F.1    Yang, L.2    Lv, F.3    Yang, Q.4    Zhou, P.5
  • 61
    • 28544451206 scopus 로고    scopus 로고
    • Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for human histocompatibility complex HLA-A0201
    • 10.1021/jm0505258, 16279801
    • Guan P, Doytchinova IA, Walshe VA, Borrow P, Flower DR. Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for human histocompatibility complex HLA-A0201. Journal of Medicinal Chemistry 2005, 48(23):7418-7425. 10.1021/jm0505258, 16279801.
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.23 , pp. 7418-7425
    • Guan, P.1    Doytchinova, I.A.2    Walshe, V.A.3    Borrow, P.4    Flower, D.R.5
  • 62
    • 79953327578 scopus 로고    scopus 로고
    • Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM)
    • 10.1007/s11030-010-9234-9, 20306130
    • Fernandez M, Caballero J, Fernandez L, Sarai A. Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM). Molecular Diversity 2011, 15(1):269-289. 10.1007/s11030-010-9234-9, 20306130.
    • (2011) Molecular Diversity , vol.15 , Issue.1 , pp. 269-289
    • Fernandez, M.1    Caballero, J.2    Fernandez, L.3    Sarai, A.4
  • 63
    • 77956814787 scopus 로고    scopus 로고
    • A novel Locally Linear Embedding and Wavelet Transform based encoding method for prediction of MHC-II binding affinity
    • Liu J, Li QJ, Zhang W. A novel Locally Linear Embedding and Wavelet Transform based encoding method for prediction of MHC-II binding affinity. Interdiscip Sci 2010, 2(2):145-150.
    • (2010) Interdiscip Sci , vol.2 , Issue.2 , pp. 145-150
    • Liu, J.1    Li, Q.J.2    Zhang, W.3
  • 64
    • 78049461176 scopus 로고    scopus 로고
    • Exploiting physico-chemical properties in string kernels
    • 10.1186/1471-2105-11-S8-S7, 3040533, 21210986
    • Toussaint NC, Widmer C, Kohlbacher O, Ratsch G. Exploiting physico-chemical properties in string kernels. BMC Bioinformatics 2010, 11(Suppl 8):S7. 10.1186/1471-2105-11-S8-S7, 3040533, 21210986.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 8
    • Toussaint, N.C.1    Widmer, C.2    Kohlbacher, O.3    Ratsch, G.4
  • 65
    • 34548458988 scopus 로고    scopus 로고
    • ProLoc: prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features
    • 10.1016/j.biosystems.2007.01.001, 17291684
    • Huang WL, Tung CW, Huang HL, Hwang SF, Ho SY. ProLoc: prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features. Biosystems 2007, 90(2):573-581. 10.1016/j.biosystems.2007.01.001, 17291684.
    • (2007) Biosystems , vol.90 , Issue.2 , pp. 573-581
    • Huang, W.L.1    Tung, C.W.2    Huang, H.L.3    Hwang, S.F.4    Ho, S.Y.5
  • 66
    • 48249145694 scopus 로고    scopus 로고
    • Computational identification of ubiquitylation sites from protein sequences
    • 10.1186/1471-2105-9-310, 2488362, 18625080
    • Tung CW, Ho SY. Computational identification of ubiquitylation sites from protein sequences. BMC Bioinformatics 2008, 9(1):310. 10.1186/1471-2105-9-310, 2488362, 18625080.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 310
    • Tung, C.W.1    Ho, S.Y.2
  • 67
    • 33644860703 scopus 로고    scopus 로고
    • Bias in error estimation when using cross-validation for model selection
    • 10.1186/1471-2105-7-91, 1397873, 16504092
    • Varma S, Simon R. Bias in error estimation when using cross-validation for model selection. BMC Bioinformatics 2006, 7:91. 10.1186/1471-2105-7-91, 1397873, 16504092.
    • (2006) BMC Bioinformatics , vol.7 , pp. 91
    • Varma, S.1    Simon, R.2
  • 68
  • 69
    • 0025855156 scopus 로고
    • Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules
    • 10.1038/351290a0, 1709722
    • Falk K, Rotzschke O, Stevanovic S, Jung G, Rammensee HG. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 1991, 351(6324):290-296. 10.1038/351290a0, 1709722.
    • (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
  • 70
    • 0016708277 scopus 로고
    • Amino acid properties and side-chain orientation in proteins: a cross correlation appraoch
    • 10.1016/0022-5193(75)90031-4, 1127956
    • Jones DD. Amino acid properties and side-chain orientation in proteins: a cross correlation appraoch. J Theor Biol 1975, 50(1):167-183. 10.1016/0022-5193(75)90031-4, 1127956.
    • (1975) J Theor Biol , vol.50 , Issue.1 , pp. 167-183
    • Jones, D.D.1
  • 71
    • 0023731964 scopus 로고
    • Amino acid side chain parameters for correlation studies in biology and pharmacology
    • Fauchere JL, Charton M, Kier LB, Verloop A, Pliska V. Amino acid side chain parameters for correlation studies in biology and pharmacology. Int J Pept Protein Res 1988, 32(4):269-278.
    • (1988) Int J Pept Protein Res , vol.32 , Issue.4 , pp. 269-278
    • Fauchere, J.L.1    Charton, M.2    Kier, L.B.3    Verloop, A.4    Pliska, V.5
  • 73
    • 0033504423 scopus 로고    scopus 로고
    • Structural, biochemical, and biophysical studies of HLA-A2/altered peptide ligands binding to viral-peptide-specific human T-cell receptors
    • 10.1101/sqb.1999.64.235, 11232291
    • Baker BM, Ding YH, Garboczi DN, Biddison WE, Wiley DC. Structural, biochemical, and biophysical studies of HLA-A2/altered peptide ligands binding to viral-peptide-specific human T-cell receptors. Cold Spring Harb Symp Quant Biol 1999, 64:235-241. 10.1101/sqb.1999.64.235, 11232291.
    • (1999) Cold Spring Harb Symp Quant Biol , vol.64 , pp. 235-241
    • Baker, B.M.1    Ding, Y.H.2    Garboczi, D.N.3    Biddison, W.E.4    Wiley, D.C.5
  • 74
    • 33644520261 scopus 로고    scopus 로고
    • BALLView: an object-oriented molecular visualization and modeling framework
    • 10.1007/s10822-005-9027-x, 16470421
    • Moll A, Hildebrandt A, Lenhof HP, Kohlbacher O. BALLView: an object-oriented molecular visualization and modeling framework. J Comput Aided Mol Des 2005, 19(11):791-800. 10.1007/s10822-005-9027-x, 16470421.
    • (2005) J Comput Aided Mol Des , vol.19 , Issue.11 , pp. 791-800
    • Moll, A.1    Hildebrandt, A.2    Lenhof, H.P.3    Kohlbacher, O.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.