메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE IMMUNE RESPONSE; AUTOIMMUNE DISORDER; BINDING AFFINITIES; EXPERIMENTAL CHARACTERIZATION; PARAMETER CONSTRAINTS; PEPTIDE FRAGMENTS; PREDICTION METHODS; THERMODYNAMIC MODEL;

EID: 77649176463     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-41     Document Type: Article
Times cited : (27)

References (43)
  • 1
    • 33645290018 scopus 로고    scopus 로고
    • MHC class II proteins and disease: a structural perspective
    • 10.1038/nri1805, 16557259
    • Jones EY, Fugger L, Strominger JL, Siebold C. MHC class II proteins and disease: a structural perspective. Nat Rev Immunol 2006, 6(4):271-282. 10.1038/nri1805, 16557259.
    • (2006) Nat Rev Immunol , vol.6 , Issue.4 , pp. 271-282
    • Jones, E.Y.1    Fugger, L.2    Strominger, J.L.3    Siebold, C.4
  • 2
    • 0028943275 scopus 로고
    • The three-dimensional structure of peptide-MHC complexes
    • 10.1146/annurev.iy.13.040195.003103, 7612235
    • Madden DR. The three-dimensional structure of peptide-MHC complexes. Annu Rev Immunol 1995, 13:587-622. 10.1146/annurev.iy.13.040195.003103, 7612235.
    • (1995) Annu Rev Immunol , vol.13 , pp. 587-622
    • Madden, D.R.1
  • 3
    • 0027937713 scopus 로고
    • Precise prediction of major histocompatibility complex class II-peptide interaction based on peptide side chain scanning
    • 10.1084/jem.180.6.2353, 2191799, 7964508
    • Hammer J, Bono E, Gallazzi F, Belunis C, Nagy Z, Sinigaglia F. Precise prediction of major histocompatibility complex class II-peptide interaction based on peptide side chain scanning. J Exp Med 1994, 180(6):2353-2358. 10.1084/jem.180.6.2353, 2191799, 7964508.
    • (1994) J Exp Med , vol.180 , Issue.6 , pp. 2353-2358
    • Hammer, J.1    Bono, E.2    Gallazzi, F.3    Belunis, C.4    Nagy, Z.5    Sinigaglia, F.6
  • 6
    • 0036137241 scopus 로고    scopus 로고
    • ProPred: prediction of HLA-DR binding sites
    • 10.1093/bioinformatics/17.12.1236, 11751237
    • Singh H, Raghava GP. ProPred: prediction of HLA-DR binding sites. Bioinformatics 2001, 17(12):1236-1237. 10.1093/bioinformatics/17.12.1236, 11751237.
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1236-1237
    • Singh, H.1    Raghava, G.P.2
  • 7
    • 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
  • 9
    • 5444249860 scopus 로고    scopus 로고
    • Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles
    • 10.1007/s00251-004-0709-7, 15349703
    • 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. 10.1007/s00251-004-0709-7, 15349703.
    • (2004) Immunogenetics , vol.56 , Issue.6 , pp. 405-419
    • Reche, P.A.1    Glutting, J.P.2    Zhang, H.3    Reinherz, E.L.4
  • 10
    • 0041620259 scopus 로고    scopus 로고
    • MHCPred: A server for quantitative prediction of peptide-MHC binding
    • 10.1093/nar/gkg510, 168917, 12824380
    • Guan P, Doytchinova IA, Zygouri C, Flower DR. MHCPred: A server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res 2003, 31(13):3621-3624. 10.1093/nar/gkg510, 168917, 12824380.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3621-3624
    • Guan, P.1    Doytchinova, I.A.2    Zygouri, C.3    Flower, D.R.4
  • 11
    • 33745360682 scopus 로고    scopus 로고
    • Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique
    • 10.1021/ci050380d, 16711768
    • Hattotuwagama CK, Toseland CP, Guan P, Taylor DJ, Hemsley SL, Doytchinova IA, Flower DR. Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique. J Chem Inf Model 2006, 46(3):1491-1502. 10.1021/ci050380d, 16711768.
    • (2006) J Chem Inf Model , vol.46 , Issue.3 , pp. 1491-1502
    • Hattotuwagama, C.K.1    Toseland, C.P.2    Guan, P.3    Taylor, D.J.4    Hemsley, S.L.5    Doytchinova, I.A.6    Flower, D.R.7
  • 12
    • 2442499729 scopus 로고    scopus 로고
    • Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach
    • 10.1093/bioinformatics/bth100, 14962912
    • Nielsen M, Lundegaard C, Worning P, Hvid CS, Lamberth K, Buus S, Brunak S, Lund O. Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics 2004, 20(9):1388-1397. 10.1093/bioinformatics/bth100, 14962912.
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1388-1397
    • Nielsen, M.1    Lundegaard, C.2    Worning, P.3    Hvid, C.S.4    Lamberth, K.5    Buus, S.6    Brunak, S.7    Lund, O.8
  • 13
    • 33750990098 scopus 로고    scopus 로고
    • Prediction of MHC class II binding peptides based on an iterative learning model
    • 10.1186/1745-7580-1-6, 1325229, 16351712
    • Murugan N, Dai Y. Prediction of MHC class II binding peptides based on an iterative learning model. Immunome Res 2005, 1:6. 10.1186/1745-7580-1-6, 1325229, 16351712.
    • (2005) Immunome Res , vol.1 , pp. 6
    • Murugan, N.1    Dai, Y.2
  • 14
    • 33746218584 scopus 로고    scopus 로고
    • MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties
    • 10.1007/s00251-006-0117-2, 16832638
    • Cui J, Han LY, Lin HH, Tang ZQ, Jiang L, Cao ZW, Chen YZ. MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties. Immunogenetics 2006, 58(8):607-613. 10.1007/s00251-006-0117-2, 16832638.
    • (2006) Immunogenetics , vol.58 , Issue.8 , pp. 607-613
    • Cui, J.1    Han, L.Y.2    Lin, H.H.3    Tang, Z.Q.4    Jiang, L.5    Cao, Z.W.6    Chen, Y.Z.7
  • 15
    • 44649167715 scopus 로고    scopus 로고
    • Application of machine learning techniques in predicting MHC binders
    • full_text, 18450002
    • Lata S, Bhasin M, Raghava GP. Application of machine learning techniques in predicting MHC binders. Methods Mol Biol 2007, 409:201-215. full_text, 18450002.
    • (2007) Methods Mol Biol , vol.409 , pp. 201-215
    • Lata, S.1    Bhasin, M.2    Raghava, G.P.3
  • 16
    • 44649155161 scopus 로고    scopus 로고
    • In silico prediction of peptide-MHC binding affinity using SVRMHC
    • full_text, 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. full_text, 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
  • 17
    • 33845240573 scopus 로고    scopus 로고
    • Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores
    • 10.1186/1471-2105-7-501, 1664591, 17105666
    • Salomon J, Flower DR. Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores. BMC Bioinformatics 2006, 7:501. 10.1186/1471-2105-7-501, 1664591, 17105666.
    • (2006) BMC Bioinformatics , vol.7 , pp. 501
    • Salomon, J.1    Flower, D.R.2
  • 18
    • 34547778364 scopus 로고    scopus 로고
    • Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method
    • 10.1186/1471-2105-8-238, 1939856, 17608956
    • Nielsen M, Lundegaard C, Lund O. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics 2007, 8:238. 10.1186/1471-2105-8-238, 1939856, 17608956.
    • (2007) BMC Bioinformatics , vol.8 , pp. 238
    • Nielsen, M.1    Lundegaard, C.2    Lund, O.3
  • 19
    • 0030057418 scopus 로고    scopus 로고
    • The nature of cryptic epitopes within the self-antigen myelin basic protein
    • 10.1093/intimm/8.7.1035, 8757949
    • Fairchild PJ, Pope H, Wraith DC. The nature of cryptic epitopes within the self-antigen myelin basic protein. Int Immunol 1996, 8(7):1035-1043. 10.1093/intimm/8.7.1035, 8757949.
    • (1996) Int Immunol , vol.8 , Issue.7 , pp. 1035-1043
    • Fairchild, P.J.1    Pope, H.2    Wraith, D.C.3
  • 20
    • 0033554853 scopus 로고    scopus 로고
    • Ovalbumin(323-339) peptide binds to the major histocompatibility complex class II I-A(d) protein using two functionally distinct registers
    • 10.1021/bi991393l, 10600129
    • McFarland BJ, Sant AJ, Lybrand TP, Beeson C. Ovalbumin(323-339) peptide binds to the major histocompatibility complex class II I-A(d) protein using two functionally distinct registers. Biochemistry 1999, 38(50):16663-16670. 10.1021/bi991393l, 10600129.
    • (1999) Biochemistry , vol.38 , Issue.50 , pp. 16663-16670
    • McFarland, B.J.1    Sant, A.J.2    Lybrand, T.P.3    Beeson, C.4
  • 21
    • 0036172037 scopus 로고    scopus 로고
    • Influence of a dominant cryptic epitope on autoimmune T cell tolerance
    • 10.1038/ni756, 11812995
    • Anderton SM, Viner NJ, Matharu P, Lowrey PA, Wraith DC. Influence of a dominant cryptic epitope on autoimmune T cell tolerance. Nat Immunol 2002, 3(2):175-181. 10.1038/ni756, 11812995.
    • (2002) Nat Immunol , vol.3 , Issue.2 , pp. 175-181
    • Anderton, S.M.1    Viner, N.J.2    Matharu, P.3    Lowrey, P.A.4    Wraith, D.C.5
  • 22
    • 1242293080 scopus 로고    scopus 로고
    • Peptide register shifting within the MHC groove: theory becomes reality
    • 10.1016/j.molimm.2003.11.016, 15036907
    • Bankovich AJ, Girvin AT, Moesta AK, Garcia KC. Peptide register shifting within the MHC groove: theory becomes reality. Mol Immunol 2004, 40(14-15):1033-1039. 10.1016/j.molimm.2003.11.016, 15036907.
    • (2004) Mol Immunol , vol.40 , Issue.14-15 , pp. 1033-1039
    • Bankovich, A.J.1    Girvin, A.T.2    Moesta, A.K.3    Garcia, K.C.4
  • 23
    • 0001287271 scopus 로고    scopus 로고
    • Regression shinkage and selection via the lasso
    • Tibshirani R. Regression shinkage and selection via the lasso. J Royal Statist Soc B 1996, 58(1):267-288.
    • (1996) J Royal Statist Soc B , vol.58 , Issue.1 , pp. 267-288
    • Tibshirani, R.1
  • 24
    • 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
  • 25
    • 57649174707 scopus 로고    scopus 로고
    • Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research
    • 10.1186/1471-2105-9-S12-S22, 2638162, 19091022
    • 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. 10.1186/1471-2105-9-S12-S22, 2638162, 19091022.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 12
    • Lin, H.H.1    Zhang, G.L.2    Tongchusak, S.3    Reinherz, E.L.4    Brusic, V.5
  • 26
    • 54749148319 scopus 로고    scopus 로고
    • On evaluating MHC-II binding peptide prediction methods
    • 10.1371/journal.pone.0003268, 2533399, 18813344
    • El-Manzalawy Y, Dobbs D, Honavar V. On evaluating MHC-II binding peptide prediction methods. PLoS One 2008, 3(9):e3268. 10.1371/journal.pone.0003268, 2533399, 18813344.
    • (2008) PLoS One , vol.3 , Issue.9
    • El-Manzalawy, Y.1    Dobbs, D.2    Honavar, V.3
  • 27
    • 0015861774 scopus 로고
    • Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction
    • 10.1016/0006-2952(73)90196-2, 4202581
    • Cheng Y, Prusoff WH. Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. Biochem Pharmacol 1973, 22(23):3099-3108. 10.1016/0006-2952(73)90196-2, 4202581.
    • (1973) Biochem Pharmacol , vol.22 , Issue.23 , pp. 3099-3108
    • Cheng, Y.1    Prusoff, W.H.2
  • 28
    • 0003404231 scopus 로고    scopus 로고
    • AMPL: A Modeling Language for Mathematical Programming
    • Pacific Grove, CA: Thomson/Brooks/Cole, 2
    • Fourer R, Gay DM, Kernighan BW. AMPL: A Modeling Language for Mathematical Programming. 2003, Pacific Grove, CA: Thomson/Brooks/Cole, 2.
    • (2003)
    • Fourer, R.1    Gay, D.M.2    Kernighan, B.W.3
  • 30
    • 0001350119 scopus 로고
    • Algebraic connectivity of graphs
    • Fiedler M. Algebraic connectivity of graphs. Czech Math Journal 1973, 23:298-305.
    • (1973) Czech Math Journal , vol.23 , pp. 298-305
    • Fiedler, M.1
  • 31
    • 0042566833 scopus 로고
    • Laplacian of graphs and algebraic connectivity
    • Fiedler M. Laplacian of graphs and algebraic connectivity. Combinatorics and Graph Theory 1989, 25:57-71.
    • (1989) Combinatorics and Graph Theory , vol.25 , pp. 57-71
    • Fiedler, M.1
  • 32
    • 0023890867 scopus 로고
    • Measuring the accuracy of diagnostic systems
    • 10.1126/science.3287615, 3287615
    • Swets JA. Measuring the accuracy of diagnostic systems. Science 1988, 240(4857):1285-1293. 10.1126/science.3287615, 3287615.
    • (1988) Science , vol.240 , Issue.4857 , pp. 1285-1293
    • Swets, J.A.1
  • 33
    • 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
  • 34
    • 84888278097 scopus 로고    scopus 로고
    • NetMHCII 2.0 Server
    • NetMHCII 2.0 Server. , http://www.cbs.dtu.dk/services/NetMHCII/
  • 35
    • 22144458334 scopus 로고    scopus 로고
    • PREDBALB/c: a system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse
    • Web Server, 10.1093/nar/gki479, 1160239, 15980450
    • Zhang GL, Srinivasan KN, Veeramani A, August JT, Brusic V. PREDBALB/c: a system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse. Nucleic Acids Res 2005, (33 Web Server):W180-183. 10.1093/nar/gki479, 1160239, 15980450.
    • (2005) Nucleic Acids Res , Issue.33
    • Zhang, G.L.1    Srinivasan, K.N.2    Veeramani, A.3    August, J.T.4    Brusic, V.5
  • 36
    • 0032566379 scopus 로고    scopus 로고
    • T cell recognition of flanking residues of murine invariant chain-derived CLIP peptide bound to MHC class II
    • 10.1006/cimm.1998.1347, 9743557
    • Naujokas MF, Southwood S, Mathies SJ, Appella E, Sette A, Miller J. T cell recognition of flanking residues of murine invariant chain-derived CLIP peptide bound to MHC class II. Cell Immunol 1998, 188(1):49-54. 10.1006/cimm.1998.1347, 9743557.
    • (1998) Cell Immunol , vol.188 , Issue.1 , pp. 49-54
    • Naujokas, M.F.1    Southwood, S.2    Mathies, S.J.3    Appella, E.4    Sette, A.5    Miller, J.6
  • 37
    • 0030047929 scopus 로고    scopus 로고
    • A study of complexes of class II invariant chain peptide: major histocompatibility complex class II molecules using a new complex-specific monoclonal antibody
    • 10.1002/eji.1830260218, 8617308
    • Eastman S, Deftos M, DeRoos PC, Hsu DH, Teyton L, Braunstein NS, Hackett CJ, Rudensky A. A study of complexes of class II invariant chain peptide: major histocompatibility complex class II molecules using a new complex-specific monoclonal antibody. Eur J Immunol 1996, 26(2):385-393. 10.1002/eji.1830260218, 8617308.
    • (1996) Eur J Immunol , vol.26 , Issue.2 , pp. 385-393
    • Eastman, S.1    Deftos, M.2    DeRoos, P.C.3    Hsu, D.H.4    Teyton, L.5    Braunstein, N.S.6    Hackett, C.J.7    Rudensky, A.8
  • 38
    • 84888284747 scopus 로고    scopus 로고
    • MHC2Pred prediction server
    • MHC2Pred prediction server. , http://imtech.res.in/raghava/mhc2pred/
  • 39
    • 70449359806 scopus 로고    scopus 로고
    • NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction
    • 2753847, 19765293
    • Nielsen M, Lund O. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics 2009, 10(296). 2753847, 19765293.
    • (2009) BMC Bioinformatics , vol.10 , Issue.296
    • Nielsen, M.1    Lund, O.2
  • 40
    • 42949139524 scopus 로고    scopus 로고
    • A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach
    • 10.1371/journal.pcbi.1000048, 2267221, 18389056
    • Wang P, Sidney J, Dow C, Mothe B, Sette A, Peters B. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol 2008, 4(4):e1000048. 10.1371/journal.pcbi.1000048, 2267221, 18389056.
    • (2008) PLoS Comput Biol , vol.4 , Issue.4
    • Wang, P.1    Sidney, J.2    Dow, C.3    Mothe, B.4    Sette, A.5    Peters, B.6
  • 41
    • 48249083459 scopus 로고    scopus 로고
    • Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan
    • 10.1371/journal.pcbi.1000107, 2430535, 18604266
    • Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O. Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol 2008, 4(7):e1000107. 10.1371/journal.pcbi.1000107, 2430535, 18604266.
    • (2008) PLoS Comput Biol , vol.4 , Issue.7
    • Nielsen, M.1    Lundegaard, C.2    Blicher, T.3    Peters, B.4    Sette, A.5    Justesen, S.6    Buus, S.7    Lund, O.8
  • 42
    • 34249803281 scopus 로고    scopus 로고
    • Cooperativity of hydrophobic anchor interactions: evidence for epitope selection by MHC class II as a folding process
    • Ferrante A, Gorski J. Cooperativity of hydrophobic anchor interactions: evidence for epitope selection by MHC class II as a folding process. J Immunol 2007, 178(11):7181-7189.
    • (2007) J Immunol , vol.178 , Issue.11 , pp. 7181-7189
    • Ferrante, A.1    Gorski, J.2
  • 43
    • 70349240535 scopus 로고    scopus 로고
    • The binding of antigenic peptides to HLA-DR is influenced by interactions between pocket 6 and pocket 9
    • 10.4049/jimmunol.0802228, 19648278
    • James EA, Moustakas AK, Bui J, Nouv R, Papadopoulos GK, Kwok WW. The binding of antigenic peptides to HLA-DR is influenced by interactions between pocket 6 and pocket 9. J Immunol 2009, 183(5):3249-3258. 10.4049/jimmunol.0802228, 19648278.
    • (2009) J Immunol , vol.183 , Issue.5 , pp. 3249-3258
    • James, E.A.1    Moustakas, A.K.2    Bui, J.3    Nouv, R.4    Papadopoulos, G.K.5    Kwok, W.W.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.