PRED^NOD, a prediction server for peptide binding to the H-2^g7 haplotype of the non-obese diabetic mouse

References

• Cresswell P, Ackerman AL, Giodini A, Peaper DR, Wearsch PA. Mechanisms of MHC class I-restricted antigen processing and cross-presentation. Immunol Rev 2005; 207: 145–157
   PubMed Web of Science ®Google Scholar
• Li P, Gregg JL, Wang N, Zhou D, O'Donnell P, Blum JS, Crotzer VL. Compartmentalization of class II antigen presentation: Contribution of cytoplasmic and endosomal processing. Immunol Rev 2005; 207: 206–217
   PubMed Web of Science ®Google Scholar
• Pamer E, Cresswell P. Mechanisms of MHC class I—restricted antigen processing. Annu Rev Immunol 1998; 16: 323–358
   PubMed Web of Science ®Google Scholar
• Villadangos JA, Bryant RA, Deussing J, Driessen C. Proteases involved in MHC class II antigen presentation. Immunol Rev 1999; 172: 109–120
   PubMed Web of Science ®Google Scholar
• Yewdell JW, Bennink JR. Cut and trim: Generating MHC class I peptide ligands. Curr Opin Immunol 2001; 13: 13–18
   PubMed Web of Science ®Google Scholar
• Bryant P, Ploegh H. Class II MHC peptide loading by the professionals. Curr Opin Immunol 2004; 16: 96–102
   PubMed Web of Science ®Google Scholar
• Zhong W, Reche PA, Lai CC, Reinhold B, Reinherz EL. Genome-wide characterization of a viral cytotoxic T lymphocyte epitope repertoire. J Biol Chem 2003; 278: 45135–45144
   PubMed Web of Science ®Google Scholar
• Brusic V, Zeleznikow J. Computational binding assays of antigenic peptides. Lett Pept Sci 1999; 6: 313–324
   Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• De Groot AS, Saint-Aubin C, Bosma A, Sbai H, Rayner J, Martin W. Rapid determination of HLA B*07 ligands from the west nile virus NY99 genome. Emerg Infect Dis 2001; 7: 706–713
   PubMed Web of Science ®Google Scholar
• Alyanakian MA, You S, Damotte D, Gouarin C, Esling A, Garcia C, Havouis S, Chatenoud L, Bach JF. Diversity of regulatory CD4+T cells controlling distinct organ-specific autoimmune diseases. Proc Natl Acad Sci USA 2003; 100: 15806–15811
   PubMed Web of Science ®Google Scholar
• Aoki CA, Borchers AT, Ridgway WM, Keen CL, Ansari AA, Gershwin ME. Autoimmun Rev 2005; 4: 373–379
   PubMed Web of Science ®Google Scholar
• Aly T, Devendra D, Eisenbarth GS. Immunotherapeutic approaches to prevent, ameliorate, and cure type 1 diabetes. Am J Ther 2005; 12: 481–490
   PubMedGoogle Scholar
• Tisch R, McDevitt H. Insulin-dependent diabetes mellitus. Cell 1996; 85: 291–297
   PubMed Web of Science ®Google Scholar
• Stratmann T, Apostolopoulos V, Mallet-Designe V, Corper AL, Scott CA, Wilson IA, Kang AS, Teyton L. The I-Ag7 MHC class II molecule linked to murine diabetes is a promiscuous peptide binder. Immunology 2000; 165: 3214–3225
   Web of Science ®Google Scholar
• Rammensee HG, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S. SYFPEITHI: Database for MHC ligands and peptide motifs. Immunogenetics 1999; 50: 213–219
   PubMed Web of Science ®Google Scholar
• Reche PA, Glutting JP, Reinherz EL. Prediction of MHC class I binding peptides using profile motifs. Hum Immunol 2002; 63: 701–709
   PubMed Web of Science ®Google Scholar
• Udaka K, Wiesmuller K, Kienle S, Jung G, Takamura H, Yamagishi H, Okumura K, Walden P, Suto T, Kawasaki T. An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries. Immunogenetics 2000; 51: 816–828
   PubMed Web of Science ®Google Scholar
• Zhang G, Srinivasan KN, Veeramani A, August T, 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: W180–W183
   PubMed Web of Science ®Google Scholar
• Reich EP, von Grafenstein H, Barlow A, Swenson KE, Williams K, Janeway CA. Self peptides isolated from MHC glycoproteins of non-obese diabetic mice. J Immunol 1994; 152: 2279–2288
   PubMed Web of Science ®Google Scholar
• Amor S, O'Neill JK, Morris MM, Smith RM, Wraith DC, Groome N, Travers PJ, Baker D. Encephalitogenic epitopes of myelin basic protein, proteolipid proteing, and myelin oligodendrocyte glycoprotein for experimental allergic en-cephalomyelitis induction in Biozzi AB/H(H-2Ag7) mice share an amino acid motif. Immunology 1996; 156: 3000–3008
   Web of Science ®Google Scholar
• Reizis B, Eisenstein M, Bockova J, Konene-Waisman S, Mor F, Elias D, Cohen IR. Molecular characterization of the diabetes mouse MHC class-II protein, I-Ag7. Int Immunol 1997; 9: 43–51
   PubMed Web of Science ®Google Scholar
• Harrison LC, Honeyman MC, Trembleau S, Gregori S, Gallazzi F, Augestein P, Brusic V, Hammer J, Adorini L. A peptide binding motif for I-Ag7, the class II major histocompatibility complex (MHC) molecule of NOD and Biozzi AB/H mice. J Exp Med 1997; 185: 1013–1021
   PubMed Web of Science ®Google Scholar
• Latek RR, Suri A, Petzold SJ, Nelson CA, Kanagawa O, Unanue ER, Fremont DH. Structural basis of peptide binding and presentation by the type I diabetes-associated MHC class II molecule of NOD mice. Immunity 2000; 12: 699–710
   PubMed Web of Science ®Google Scholar
• Corper AL, Stratmann T, Apostolopoulos V, Scott CA, Garcia KC, Kang AS, Wilson IA, Tevton L. A structural framework for deciphering the link between I-Ag7 and autoimmune diabetes. Science 2000; 288: 505–511
   PubMed Web of Science ®Google Scholar
• Gregori S, Bono E, Gallazzi F, Hammer J, Harrison LC, Adorini L. The motif for peptide binding to the insulin-dependent diabetes mellitus-associated class II MHC molecule I-Ag7 validated by phage display library. Int Immunol 2000; 12: 493–503
   PubMed Web of Science ®Google Scholar
• Rajapakse M, Wyse L, Schmidt B, Brusic V. Deriving matrix of peptide interactions in diabetic mouse by genetic algorithm. Lect Notes Comp Sci 2005; 3578: 440–447
   Google Scholar
• Swets JA. Measuring the accuracy of diagnostic systems. Science 1998; 240: 1285–1293
   Web of Science ®Google Scholar
• Yu B, et al. Binding of conserved islet peptides by human and murine MHC class II molecules associated with susceptibility to type I diabetes. J Immunol 2000; 30: 2497–2506
   Web of Science ®Google Scholar
• Brusic V, Rudy G, Harrison LC. MHCPEP, a database of MHC-binding peptides. Nucleic Acids Res 1994; 22: 3663–3665
   PubMed Web of Science ®Google Scholar
• Bhasin M, Singh H, Raghava GP. MHCBN: A comprehensive database of MHC binding and non-binding peptides. Bioinformatics 2003; 19: 665–666
   PubMed Web of Science ®Google Scholar
• McSparron H, Blythe MJ, Zygouri C, Doytchinova IA, Flower DR. JenPep: A novel computational information resource for immunobiology and vaccinology. J Chem Inf Comput Sci 2004; 43: 1276–1287
   Google Scholar
• Rammensee HG, Falk K, Rotzschke O. Peptides naturally presented by MHC class I molecules. Annu Rev Immunol 1993; 11: 213–244
   PubMed Web of Science ®Google Scholar
• Yu K, Petrovsky N, Schönbach C, Koh JYL, Brusic V. Methods for prediction of peptide binding to MHC molecules: A comparative study. Mol Med 2002; 8: 137–148
   PubMed Web of Science ®Google Scholar
• Quesnel A, Hsu SC, Delmas A, Steward MW, Trudelle Y, Abastado JP. Efficient binding to the MHC class I K(d) molecule of synthetic peptides in which the anchoring position 2 does not fit the consensus motif. FEBS Lett 1996; 387: 42–46
   PubMed Web of Science ®Google Scholar
• Sette A, Buus S, Appella E, Smith JA, Chesnut R, Miles C, Colon SM, Grey HM. Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis. Proc Natl Acad Sci USA 1989; 86: 3296–3300
   PubMed Web of Science ®Google Scholar
• Mata M, Travers PJ, Liu Q, Frankel FR, Paterson Y. The MHC class I-restricted immune response to HIV-gag in BALB/c mice selects a single epitope that does not have a predictable MHC-binding motif and binds to Kd through interactions between a glutamine at P3 and pocket D1. J Immunol 1998; 161: 2985–2993
   PubMed Web of Science ®Google Scholar
• Saikh KU, Martin JD, Nishikawa AH, Dillon SB. Influenza A virus-specific H-2d restricted cross-reactive cytotoxic T lymphocyte epitope(s) detected in the hemagglutinin HA2 subunit of A/Udorn/72. Virology 1995; 214: 445–452
   PubMed Web of Science ®Google Scholar
• Zatechka DS, Jr, Hegde NR, Hariharan K, Srikumaran S. Identification of murine cytotoxic T-lymphocyte epitopes of bovine herpesvirus 1. Vaccine 1999; 17: 686–694
   PubMed Web of Science ®Google Scholar
• Pe'er I, et al. Proteomic signatures: Amino acid and oligopeptide compositions differentiate among phyla. Proteins 2004; 54: 20–40
   PubMed Web of Science ®Google Scholar
• Reche PA, Glutting JP, Reinherz EL. Prediction of MHC class I binding peptides using profile motifs. Hum Immunol 2002; 63: 701–709
   PubMed Web of Science ®Google Scholar
• Reche PA, Zhang H, Glutting JP, Reinherz EL. EPIMHC: A curated database of MHC-binding peptides for customized computational vaccinology. Bioinformatics 2005; 21: 2140–2141
   PubMed Web of Science ®Google Scholar
• Lyman M, Lee H, Kang B, Kang H, Kim B. Capsid-specific cytotoxic T lymphocytes recognize three distinct H-2D(b)-restricted regions of the BeAn strain of Theiler's virus and exhibit different cytokine profiles. J Virol 2002; 76: 3125–3134
   PubMed Web of Science ®Google Scholar
• Saren A, Pascolo S, Stevanovic S, et al. Identification of Chlamydia pneumoniae-derived mouse CD8 epitopes. Infect Immun 2002; 70: 3336–3343
   PubMed Web of Science ®Google Scholar
• Sigal L, Goebel P, Wylie D. Db-binding peptides from influenza virus: Effect of non-anchor residues on stability and immunodominance. Mol Immunol 1995; 32: 623–632
   PubMed Web of Science ®Google Scholar
• Hudrisier D, Mazarguil H, Laval F, Oldstone M, Gairin J. Binding of viral antigens to major histocompatibility complex class I H-2Db molecules is controlled by dominant negative elements at peptide non-anchor residues: Implications for peptide selection and presentation. J Biol Chem 1996; 271: 17829–17836
   PubMed Web of Science ®Google Scholar
• Blythe MJ, Doytchinova IA, Flower DR. JenPep: A database of quantitative functional peptide data for immunology. Bioinformatics 2002; 18: 434–439
   PubMed Web of Science ®Google Scholar
• Gupta V, Tabiin TM, Sun K, Chandrasekaran A, Anwar A, Yang K, Chikhlikar P, Salmon J, Brusic V, Marques ET, Kellathur SN, August TJ. SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens. Virology 2006; 347: 27–39
   Web of Science ®Google Scholar
• Suri A, Walters JJ, Levisetti MG, Gross ML, Unanue ER. Identification of naturally processed peptides bound to the class I MHC molecule H-2Kd of normal and TAP-deficient cells. Eur J Immunol 2006; 36(3)544–557
   PubMed Web of Science ®Google Scholar
• Suri A, et al. In APCs, the autologous peptides selected by the diabetogenic I-Ag7 molecule are unique and determined by the amino acid changes in the P9 pocket. J Immunol 2002; 168: 1235–1243
   PubMed Web of Science ®Google Scholar