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Volumn 9, Issue 6, 2013, Pages

Scrutinizing MHC-I Binding Peptides and Their Limits of Variation

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; EPITOPES; FORECASTING; LEARNING ALGORITHMS; LEARNING SYSTEMS;

EID: 84879540457     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003088     Document Type: Article
Times cited : (32)

References (64)
  • 2
    • 17644416719 scopus 로고    scopus 로고
    • Targeting the innate immune response with improved vaccine adjuvants
    • Pashine A, Valiante NM, Ulmer JB, (2005) Targeting the innate immune response with improved vaccine adjuvants. Nat Med 11: S63-S68.
    • (2005) Nat Med , vol.11
    • Pashine, A.1    Valiante, N.M.2    Ulmer, J.B.3
  • 4
    • 79952943828 scopus 로고    scopus 로고
    • Fundamentals of vaccine immunology
    • Clem AS, (2011) Fundamentals of vaccine immunology. J Global Infect Dis 3: 73-78.
    • (2011) J Global Infect Dis , vol.3 , pp. 73-78
    • Clem, A.S.1
  • 6
    • 0030842457 scopus 로고    scopus 로고
    • Design of peptide and polypeptide vaccines
    • Ben-Yedidia T, Arnon R, (1997) Design of peptide and polypeptide vaccines. Curr Opin Biotechnol 8: 442-448.
    • (1997) Curr Opin Biotechnol , vol.8 , pp. 442-448
    • Ben-Yedidia, T.1    Arnon, R.2
  • 7
    • 0027369601 scopus 로고
    • Synthetic peptide vaccines
    • Sesardic D, (1993) Synthetic peptide vaccines. J Med Microbiol 39: 241-242.
    • (1993) J Med Microbiol , vol.39 , pp. 241-242
    • Sesardic, D.1
  • 9
    • 0027399243 scopus 로고
    • Peptides naturally presented by MHC class I molecules
    • Rammensee HG, Falk K, Rötzschke O, (1993) Peptides naturally presented by MHC class I molecules. Annu Rev Immunol 11: 213-244.
    • (1993) Annu Rev Immunol , vol.11 , pp. 213-244
    • Rammensee, H.G.1    Falk, K.2    Rötzschke, O.3
  • 11
    • 33745584371 scopus 로고    scopus 로고
    • A community resource benchmarking predictions of peptide binding to MHC-I molecules
    • Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, et al. (2006) A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol 2: e65.
    • (2006) PLoS Comput Biol , vol.2
    • Peters, B.1    Bui, H.H.2    Frankild, S.3    Nielson, M.4    Lundegaard, C.5
  • 12
    • 34047232962 scopus 로고    scopus 로고
    • Design of MHC I stabilizing peptides by agent-based exploration of sequence space
    • Hiss JA, Bredenbeck A, Losch FO, Wrede P, Walden P, et al. (2007) Design of MHC I stabilizing peptides by agent-based exploration of sequence space. Prot Eng Des Sel 20: 99-108.
    • (2007) Prot Eng Des Sel , vol.20 , pp. 99-108
    • Hiss, J.A.1    Bredenbeck, A.2    Losch, F.O.3    Wrede, P.4    Walden, P.5
  • 16
    • 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, et al. (1993) 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 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
  • 17
    • 0035452568 scopus 로고    scopus 로고
    • Use of fluorescence polarization to monitor MHC-peptide interactions in solution
    • Dédier S, Reinelt S, Rion S, Folkers G, Rognan D, (2001) Use of fluorescence polarization to monitor MHC-peptide interactions in solution. J Immunol Methods 255: 57-66.
    • (2001) J Immunol Methods , vol.255 , pp. 57-66
    • Dédier, S.1    Reinelt, S.2    Rion, S.3    Folkers, G.4    Rognan, D.5
  • 18
  • 19
    • 0029005514 scopus 로고
    • Decrypting the structure of major histocompatibility complex class I-restricted cytotoxic T lymphocyte epitopes with complex peptide libraries
    • Udaka K, Wiesmüller KH, Kienle S, Jung G, Walden P, (1995) Decrypting the structure of major histocompatibility complex class I-restricted cytotoxic T lymphocyte epitopes with complex peptide libraries. J Exp Med 181: 2097-2108.
    • (1995) J Exp Med , vol.181 , pp. 2097-2108
    • Udaka, K.1    Wiesmüller, K.H.2    Kienle, S.3    Jung, G.4    Walden, P.5
  • 20
    • 0034660206 scopus 로고    scopus 로고
    • The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site
    • Khan AR, Baker BM, Ghosh P, Biddison WE, Wiley DC, (2000) The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site. J Immunol 164: 6398-6405.
    • (2000) J Immunol , vol.164 , pp. 6398-6405
    • Khan, A.R.1    Baker, B.M.2    Ghosh, P.3    Biddison, W.E.4    Wiley, D.C.5
  • 21
    • 54749148319 scopus 로고    scopus 로고
    • On evaluating MHC-II binding peptide prediction methods
    • El-Manzalawy Y, Drobbs D, Honavar V, (2008) On evaluating MHC-II binding peptide prediction methods. PLOS One 3: e3268.
    • (2008) PLOS One , vol.3
    • El-Manzalawy, Y.1    Drobbs, D.2    Honavar, V.3
  • 22
    • 77956964002 scopus 로고    scopus 로고
    • Best practices for QSAR model development, validation, and exploitation
    • Tropsha A, (2010) Best practices for QSAR model development, validation, and exploitation. Mol Inf 29: 476-488.
    • (2010) Mol Inf , vol.29 , pp. 476-488
    • Tropsha, A.1
  • 24
    • 34249753618 scopus 로고
    • Support-vector networks
    • Cortes C, Vapnik V, (1995) Support-vector networks. Machine Learning 20: 273-297.
    • (1995) Machine Learning , vol.20 , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 25
    • 0022471098 scopus 로고
    • Learning representations by back-propagating errors
    • Rumelhart DE, Hinton GE, Williams RJ, (1986) Learning representations by back-propagating errors. Nature 323: 533-536.
    • (1986) Nature , vol.323 , pp. 533-536
    • Rumelhart, D.E.1    Hinton, G.E.2    Williams, R.J.3
  • 26
    • 84898983292 scopus 로고    scopus 로고
    • Using analytic QP and sparseness to speed training of support vector machines
    • Platt JC, (1999) Using analytic QP and sparseness to speed training of support vector machines. Adv Neural Inf Proc Syst 11: 557-563.
    • (1999) Adv Neural Inf Proc Syst , vol.11 , pp. 557-563
    • Platt, J.C.1
  • 27
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews BW, (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 405: 442-451.
    • (1975) Biochim Biophys Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 28
    • 84870267223 scopus 로고
    • The generalization of student's' problem when several different population variances are involved
    • Welch BL, (1947) The generalization of student's' problem when several different population variances are involved. Biometrika 34: 28-35.
    • (1947) Biometrika , vol.34 , pp. 28-35
    • Welch, B.L.1
  • 29
    • 0028943275 scopus 로고
    • The three-dimensional structure of peptide-MHC complexes
    • Madden DR, (1995) The three-dimensional structure of peptide-MHC complexes. Annu Rev Immunol 13: 587-622.
    • (1995) Annu Rev Immunol , vol.13 , pp. 587-622
    • Madden, D.R.1
  • 30
    • 0027241255 scopus 로고
    • Amino acid changes in the peptide binding site have structural consequences at the surface of class I glycoproteins
    • Pease LR, Horton RM, Pullen JK, Hunt HD, Yun TJ, et al. (1993) Amino acid changes in the peptide binding site have structural consequences at the surface of class I glycoproteins. J Immunol 150: 3375-3381.
    • (1993) J Immunol , vol.150 , pp. 3375-3381
    • Pease, L.R.1    Horton, R.M.2    Pullen, J.K.3    Hunt, H.D.4    Yun, T.J.5
  • 31
    • 0028135684 scopus 로고
    • Molecular dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes
    • Rognan D, Scapozza L, Folkers G, Daser A, (1994) Molecular dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes. Biochemistry 33: 11476-11485.
    • (1994) Biochemistry , vol.33 , pp. 11476-11485
    • Rognan, D.1    Scapozza, L.2    Folkers, G.3    Daser, A.4
  • 33
    • 0344352477 scopus 로고    scopus 로고
    • Contribution of peptide backbone atoms to binding of an antigenic peptide to class I major histocompatibility complex molecules
    • Satio NG, Paterson Y, (1997) Contribution of peptide backbone atoms to binding of an antigenic peptide to class I major histocompatibility complex molecules. Mol Immunol 34: 1133-1145.
    • (1997) Mol Immunol , vol.34 , pp. 1133-1145
    • Satio, N.G.1    Paterson, Y.2
  • 34
    • 0027170190 scopus 로고
    • Differential amino-terminal anchors for peptide binding to H-2M3a or H-2Kb and H-2Db1
    • Shawar SM, Vyas JM, Shen E, Rogers JR, Rich RR, (1993) Differential amino-terminal anchors for peptide binding to H-2M3a or H-2Kb and H-2Db1. J Immunol 151: 201-210.
    • (1993) J Immunol , vol.151 , pp. 201-210
    • Shawar, S.M.1    Vyas, J.M.2    Shen, E.3    Rogers, J.R.4    Rich, R.R.5
  • 35
    • 0345493812 scopus 로고    scopus 로고
    • Binding of longer peptides to the H-2Kb heterodimer is restricted to peptides extended at their C-terminus: refinement of inherent MHC class I peptide binding criteria
    • Hörig H, Young ACM, Papadopoulos NJ, DiLorenzo TP, Natheson SG, (1999) Binding of longer peptides to the H-2Kb heterodimer is restricted to peptides extended at their C-terminus: refinement of inherent MHC class I peptide binding criteria. J Immunol 163: 4434-4441.
    • (1999) J Immunol , vol.163 , pp. 4434-4441
    • Hörig, H.1    Young, A.C.M.2    Papadopoulos, N.J.3    DiLorenzo, T.P.4    Natheson, S.G.5
  • 36
    • 0027333434 scopus 로고
    • H-2Dd exploits a four residue peptide binding motif
    • Corr M, Boyd LF, Padlan EA, Margulies DH, (1993) H-2Dd exploits a four residue peptide binding motif. J Exp Med 178: 1877-1892.
    • (1993) J Exp Med , vol.178 , pp. 1877-1892
    • Corr, M.1    Boyd, L.F.2    Padlan, E.A.3    Margulies, D.H.4
  • 37
    • 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, (2008) Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol 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
  • 38
    • 33745584371 scopus 로고    scopus 로고
    • A community resource benchmarking predictions of peptide binding to MHC-I molecules
    • Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, et al. (2006) A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol 2: e65.
    • (2006) PLoS Comput Biol , vol.2
    • Peters, B.1    Bui, H.H.2    Frankild, S.3    Nielson, M.4    Lundegaard, C.5
  • 39
    • 0031904715 scopus 로고    scopus 로고
    • Application of an artificial neural network to predict specific class I MHC binding peptide sequences
    • Milik M, Sauer D, Brunmark AP, Yuan L, Vitiello A, et al. (1998) Application of an artificial neural network to predict specific class I MHC binding peptide sequences. Nat Biotechnol 16: 753-756.
    • (1998) Nat Biotechnol , vol.16 , pp. 753-756
    • Milik, M.1    Sauer, D.2    Brunmark, A.P.3    Yuan, L.4    Vitiello, A.5
  • 41
    • 0029096589 scopus 로고
    • Prediction of binding to MHC class I molecules
    • Adams HP, Koziol JA, (1995) Prediction of binding to MHC class I molecules. J Immunol Methods 185: 181-190.
    • (1995) J Immunol Methods , vol.185 , pp. 181-190
    • Adams, H.P.1    Koziol, J.A.2
  • 42
    • 0031825709 scopus 로고    scopus 로고
    • Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network
    • Brusic V, Rudy G, Honeyman G, Hammer J, Harrison L, (1998) 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    Rudy, G.2    Honeyman, G.3    Hammer, J.4    Harrison, L.5
  • 43
    • 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, et al. (2008) 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.
    • (2008) Nucleic Acids Res , vol.36
    • Lundegaard, C.1    Lamberth, K.2    Harndahl, M.3    Buus, S.4    Lund, O.5
  • 45
    • 75149176174 scopus 로고    scopus 로고
    • Ensemble-based classifiers
    • Rokach L, (2010) Ensemble-based classifiers. Artif Intell Rev 33: 1-39.
    • (2010) Artif Intell Rev , vol.33 , pp. 1-39
    • Rokach, L.1
  • 46
    • 0000551189 scopus 로고    scopus 로고
    • Popular ensemble methods: An empirical study
    • Maclin R, Opitz D, (1999) Popular ensemble methods: An empirical study. J Artif Intell Res 11: 169-198.
    • (1999) J Artif Intell Res , vol.11 , pp. 169-198
    • Maclin, R.1    Opitz, D.2
  • 47
    • 0026692226 scopus 로고
    • Stacked generalization
    • Wolpert DH, (1992) Stacked generalization. Neural Networks 5: 241-259.
    • (1992) Neural Networks , vol.5 , pp. 241-259
    • Wolpert, D.H.1
  • 48
    • 84876487418 scopus 로고    scopus 로고
    • Computational resources for MHC ligand identification
    • Koch CP, Pillong M, Hiss JA, Schneider G, (2013) Computational resources for MHC ligand identification. Mol Inf 32: 326-336.
    • (2013) Mol Inf , vol.32 , pp. 326-336
    • Koch, C.P.1    Pillong, M.2    Hiss, J.A.3    Schneider, G.4
  • 50
    • 0027450354 scopus 로고
    • T cell-dependent B cell activation
    • Parker DC, (1993) T cell-dependent B cell activation. Annu Rev Immunol 11: 331-360.
    • (1993) Annu Rev Immunol , vol.11 , pp. 331-360
    • Parker, D.C.1
  • 51
    • 0027199489 scopus 로고
    • Characterization of neutralizing monoclonal antibodies to linear and conformation-dependent epitopes within the first and second variable domains of human immunodeficiency virus type 1 gp120
    • McKeating JA, Shotton C, Cordell J, Graham S, Balfe P, et al. (1993) Characterization of neutralizing monoclonal antibodies to linear and conformation-dependent epitopes within the first and second variable domains of human immunodeficiency virus type 1 gp120. J Virol 67: 4932-4944.
    • (1993) J Virol , vol.67 , pp. 4932-4944
    • McKeating, J.A.1    Shotton, C.2    Cordell, J.3    Graham, S.4    Balfe, P.5
  • 52
    • 0026642501 scopus 로고    scopus 로고
    • Molecular modeling of an antigenic complex between a viral peptide and a class I major histocompatibility glycoprotein
    • Rognan D, Reddehase MJ, Koszinowski UH, Folkers G, (2004) Molecular modeling of an antigenic complex between a viral peptide and a class I major histocompatibility glycoprotein. Proteins 13: 70-85.
    • (2004) Proteins , vol.13 , pp. 70-85
    • Rognan, D.1    Reddehase, M.J.2    Koszinowski, U.H.3    Folkers, G.4
  • 54
    • 2142730100 scopus 로고    scopus 로고
    • Central memory and effector memory T cell subsets: function, generation, and maintenance
    • Sallusto F, Geginat J, Lanzavecchia A, (2004) Central memory and effector memory T cell subsets: function, generation, and maintenance. Annu Rev Immunol 22: 745-763.
    • (2004) Annu Rev Immunol , vol.22 , pp. 745-763
    • Sallusto, F.1    Geginat, J.2    Lanzavecchia, A.3
  • 55
    • 0033523672 scopus 로고    scopus 로고
    • "Scaffold-hopping" by topological pharmacophore search: A contribution to virtual screening
    • Schneider G, Neidhart W, Giller T, Schmid G, (1999) "Scaffold-hopping" by topological pharmacophore search: A contribution to virtual screening. Angew Chem Int Ed 38: 2894-2896.
    • (1999) Angew Chem Int Ed , vol.38 , pp. 2894-2896
    • Schneider, G.1    Neidhart, W.2    Giller, T.3    Schmid, G.4
  • 56
    • 2942524875 scopus 로고    scopus 로고
    • Visualization of protein sequence space by self-organizing neural networks - Classification of protein targeting signals
    • In: Wagner E, Normann J, Greppin H, Hackstein JHP, Herrmann RG et al., editors. Geneva: Geneva University Press
    • Schneider G, Broger C (1999) Visualization of protein sequence space by self-organizing neural networks- Classification of protein targeting signals. In: Wagner E, Normann J, Greppin H, Hackstein JHP, Herrmann RG et al., editors. From Symbiosis to Eukaryotism- Endocytobiology VII. Geneva: Geneva University Press. pp. 589-602.
    • (1999) From Symbiosis to Eukaryotism - Endocytobiology VII , pp. 589-602
    • Schneider, G.1    Broger, C.2
  • 57
    • 84874101052 scopus 로고    scopus 로고
    • Chemically advanced template search (CATS) for scaffold-hopping and prospective target prediction for 'orphan' molecules
    • Reutlinger M, Koch CP, Reker D, Todoroff N, Schneider P, et al. (2013) Chemically advanced template search (CATS) for scaffold-hopping and prospective target prediction for 'orphan' molecules. Mol Inf 32: 133-138.
    • (2013) Mol Inf , vol.32 , pp. 133-138
    • Reutlinger, M.1    Koch, C.P.2    Reker, D.3    Todoroff, N.4    Schneider, P.5
  • 58
    • 0031735526 scopus 로고    scopus 로고
    • Artificial neural networks for computer-based molecular design
    • Schneider G, Wrede P, (1998) Artificial neural networks for computer-based molecular design. Prog Biophys Mol Biol 70: 175-222.
    • (1998) Prog Biophys Mol Biol , vol.70 , pp. 175-222
    • Schneider, G.1    Wrede, P.2
  • 59
    • 0029922443 scopus 로고    scopus 로고
    • Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
    • Tomii K, Kanehisa M, (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng 9: 27-36.
    • (1996) Protein Eng , vol.9 , pp. 27-36
    • Tomii, K.1    Kanehisa, M.2
  • 64
    • 0028987213 scopus 로고
    • Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove
    • Fremont DH, Stura EA, Matsumura M, Peterson PA, Wilson IA, (1995) Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove. Proc Natl Acad Sci USA 92: 2479-2483.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 2479-2483
    • Fremont, D.H.1    Stura, E.A.2    Matsumura, M.3    Peterson, P.A.4    Wilson, I.A.5


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