Computational immunology meets bioinformatics: The use of prediction tools for molecular binding in the simulation of the immune system

PLoS ONE

Volumn 5, Issue 4, 2010, Pages

  Rapin, Nicolas ^a   Lund, Ole ^b   Bernaschi, Massimo ^c   Castiglione, Filippo ^c  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; MAJOR HISTOCOMPATIBILITY ANTIGEN;

ANTIBODY TITER; ANTIGEN ANTIBODY COMPLEX; ARTICLE; BINDING AFFINITY; BIOINFORMATICS; CELL INTERACTION; CELL PROLIFERATION; COMPUTER SIMULATION; CONTROLLED STUDY; HELPER CELL; HETEROZYGOSITY; HOMOZYGOTE; IMMUNE RESPONSE; IMMUNE SYSTEM; IMMUNOGENICITY; IMMUNOLOGICAL MEMORY; INFLUENZA VIRUS; LONG TERM EXPOSURE; MATHEMATICAL MODEL; MOLECULAR CLONING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PREDICTION; PROTEIN BINDING; PROTEIN FUNCTION; SYSTEMS BIOLOGY; T LYMPHOCYTE ACTIVATION; BIOLOGICAL MODEL; BIOLOGY; CYTOLOGY; IMMUNOLOGICAL PROCEDURES; IMMUNOLOGY; METHODOLOGY;

ORTHOMYXOVIRIDAE;

ALLERGY AND IMMUNOLOGY; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EPITOPES, B-LYMPHOCYTE; EPITOPES, T-LYMPHOCYTE; IMMUNE SYSTEM; IMMUNOLOGIC TECHNIQUES; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY;

EID: 77956357957     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009862     Document Type: Article

References (85)

1. Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M (2007) Modeling the adaptive immune system: predictions and simulations. Bioinformatics 23: 3265-3275.
2. Celada F, Seiden PE (1992) A computer model of cellular interactions in the immune system. Immunol Today 13: 56-62.
3. Lund O, Nielsen M, Kesmir C, Petersen AG, Lundegaard C, et al. (2004) Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics 55: 797-810.
4. Nielsen M, Lundegaard C, Worning P, Hvid CS, Lamberth K, et al. (2004) Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics 20: 1388-1397.
5. Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, et al. (2007) NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS ONE 2: e796.
6. Nielsen M, Lundegaard C, Lund O (2007) Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics 8: 238.
7. Miyazawa S, Jernigan RL (1999) An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 36: 357-369.
8. Perelson AS, Weisbuch G (1997) Immunology for physicists. Rev Mod Phys 69: 1219-1267.
9. Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, et al. (1995) Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373: 123-126.
10. Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, et al. (1995) Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373: 117-122.
11. Wein LM, Zenios SA, Nowak MA (1997) Dynamic multidrug therapies for HIV: a control theoretic approach. J Theor Biol 185: 15-29.
12. Perelson AS, Essunger P, Cao Y, Vesanen M, Hurley A, et al. (1997) Decay characteristics of HIV-1-infected compartments during combination therapy. Nature 387: 188-191.
13. McLean AR, Nowak MA (1992) Competition between zidovudine-sensitive and zidovudine-resistant strains of HIV. AIDS 6: 71-79.
14. Perelson AS, Kirschner DE, De Boer R (1993) Dynamics of HIV infection of CD4+ T cells. Math Biosci 114: 81-125.
15. Essunger P, Perelson AS (1994) Modeling hiv infection of cd4+ t-cell subpopulations. J Theor Biol 170: 367-391.
16. Mittler JE, Levin BR, Antia R (1996) T-cell homeostasis, competition, and drift: Aids as hiv-accelerated senescence of the immune repertoire. J Acquir Immune Defic Syndr Hum Retrovirol 12: 233-248.
17. Nowak MA, Bonhoeffer S, Shaw GM, May RM (1997) Anti-viral drug treatment: dynamics of resistance in free virus and infected cell populations. J Theor Biol 184: 203-217.
18. Nowak MA, Lloyd AL, Vasquez GM, Wiltrout TA, Wahl LM, et al. (1997) Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection. J Virol 71: 7518-7525.
19. Stilianakis NI, Boucher CA, De Jong MD, Van Leeuwen R, Schuurman R, et al. (1997) Clinical data sets of human immunodeficiency virus type 1 reverse transcriptase-resistant mutants explained by a mathematical model. J Virol 71: 161-168.
20. Bonhoeffer S, May RM, Shaw GM, Nowak MA (1997) Virus dynamics and drug therapy. Proc Natl Acad Sci U S A 94: 6971-6976.
21. de Jong MD, de Boer RJ, de Wolf F, Foudraine NA, Boucher CA, et al. (1997) Overshoot of HIV-1 viraemia after early discontinuation of antiretroviral treatment. AIDS 11: F79-84.
22. Herz AV, Bonhoeffer S, Anderson RM, May RM, Nowak MA (1996) Viral dynamics in vivo: limitations on estimates of intracellular delay and virus decay. Proc Natl Acad Sci U S A 93: 7247-7251.
23. Klenerman P, Phillips RE, Rinaldo CR, Wahl LM, Ogg G, et al. (1996) Cytotoxic t lymphocytes and viral turnover in hiv type 1 infection. Proc Natl Acad Sci U S A 93: 15323-15328.
24. Seiden PE, Celada F (1992) A model for simulating cognate recognition and response in the immune system. J Theor Biol 158: 329-357.
25. Celada F, Seiden PE (1996) Affinity maturation and hypermutation in a simulation of the humoral immune response. Eur J Immunol 26: 1350-1358.
26. Morpurgo D, Serenthà R, Seiden PE, Celada F (1995) Modelling thymic functions in a cellular automaton. Int Immunol 7: 505-516.
27. Castiglione F, Poccia F, D'Offizi G, Bernaschi M (2004) Mutation, fitness, viral diversity, and predictive markers of disease progression in a computational model of HIV type 1 infection. AIDS Res Hum Retroviruses 20: 1314-1323.
28. Castiglione F, Duca K, Jarrah A, Laubenbacher R, Hochberg D, et al. (2007) Simulating epstein-barr virus infection with C-Immsim. Bioinformatics 23: 1371-1377.
29. Santoni D, Pedicini M, Castiglione F (2008) Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hyper-sensitivity reactions. Bioinformatics 24: 1374-1380.
30. Motta S, Castiglione F, Lollini PL, Pappalardo F (2005) Modelling vaccination schedules for a cancer immunoprevention vaccine. Immunome Res 1: 5.
31. Cheng Y, Ghersi D, Calcagno C, Selin LK, Puzone R, et al. (2009) A discrete computer model of the immune system reveals competitive interactions between the humoral and cellular branch and between cross-reacting memory and nave responses. Vaccine 27: 833-45.
32. Meier-Schellersheim M, Mack G (1999) Simmune, a tool for simulating and analyzing immune system behavior. URL http://www.citebase.org/abstract?id=oai:arXiv.org:cs/9903017.
33. Folcik VA, An GC, Orosz CG (2007) The basic immune simulator: an agentbased model to study the interactions between innate and adaptive immunity. Theor Biol Med Model 4: 39.
34. Kalita JK, Chandrashekar K, Hans R, Selvam P (2006) Computational modelling and simulation of the immune system. Int J Bioinform Res Appl 2: 63-88.
35. Perelson AS, Oster GF (1979) Theoretical studies of clonal selection: minimal antibody repertoire size and reliability of self-non-self discrimination. J Theor Biol 81: 645-670.
36. Farmer JD, Packard NH, Perelson AS (1986) The immune system, adaptation, and machine learning. Phys D 2: 187-204.
37. De Boer RJ, Perelson AS (1994) T cell repertoires and competitive exclusion. J Theor Biol 169: 375-390.
38. Perelson AS (1989) Immune network theory. Immunol Rev 110: 5-36.
39. Sulzer B, Perelson AS (1996) Equilibrium binding of multivalent ligands to cells: effects of cell and receptor density. Math Biosci 135: 147-185.
40. Bernaschi M, Castiglione F (2001) Evolution of an immune system simulator. Comp Biol Med 31(5): 303-31.
41. Hedrick SM, Cohen DI, Nielsen EA, Davis MM (1983) Isolation of cDNA clones encoding T cell specific membrane-associated proteins. Nature 308: 149-153.
42. Seidman JG, Leder P (1978) The arrangement and rearrangement of antibody genes. Nature 276: 790-795.
43. Tonegawa S (1983) Somatic generation of antibody diversity. Nature 302: 575-581.
44. Allen PM (1987) Antigen processing at the molecular level. Immunol Today 8: 270-273.
45. Berzofski JA (1985) The nature and role of antigen processing in t cell activation, in: Cruse JM, Lewis RE, eds. Year in Immunology 1984-1985. pp 18-24.
46. Manca F, Kunkl A, Fenoglio D, Fowler A, Sercarz E, et al. (1985) Constraints in T-B cooperation related to epitope topology on E. coli b-galactosidase. I. the fine specificity of T cells dictates the fine specificity of antibodies directed to conformation-dependent determinants. Eur J Immunol 15: 345-350.
47. Unanue ER (1984) Antigen-presenting function of the macrophage. Ann Rev Immunol 2: 395-428.
48. Haskins K, Kubo R, White J, Pigeon M, Kappler J, et al. (1983) The major histocompatibility complex-restricted antigen receptor on T cells. J Exp Med 157: 1149-1162.
49. Howard JC (1985) Immunological help at last. Nature 314: 494-495.
50. Lanzavecchia A (1985) Antigen-specific interactions between T and B cells. Nature 314: 537-539.
51. Berek C, Ziegner M (1993) The maturation of the immune response. Immunol Today 14: 400-404.
52. Celada F (1971) The cellular basis of immunological memory. Prog Allergy 15: 223-267.
53. Burnet FM (1959) The Clonal Selection Theory of Acquired Immunity. Cambridge: Cambridge University Press.
54. Sprent J, Lo D, Gao EK, Ron Y (1988) T cell selection in the thymus. Immunol Rev 101: 173-190.
55. Hayflick L, Moorhead PS (1961) The serial cultivation of human diploid cell strains. Exp Cell Res 25: 585-621.
56. Hayflick L (1965) The limited in vitro lifetime of human diploid cell strains. Exp Cell Res 37: 614-636.
57. Shay JW, Wright WE (2000) Hayflick, his limit, and cellular ageing. Nat Rev Mol Cell Biol 1: 72-6.
58. Effros RB, Pawelec G (1997) Replicative senescence of T cells: does the Hayflick limit lead to immune exhaustion? Immunol Today 18: 450-454.
59. Nossal GJ, Pike BL (1980) Clonal anergy: persistence in tolerant mice of antigenbinding B lymphocytes incapable of responding to antigen or mitogen. Proc Natl Acad Sci U S A 77: 1602-1606.
60. Whitacre CC, Gienapp IE, Orosz CG, Bitar DM (1991) Oral tolerance in experimental autoimmune encephalomyelitis. III. evidence for clonal anergy. J Immunol 147: 2155-2163.
61. Schwartz RH (2003) T cell anergy. Annu Rev Immunol 21: 305-334.
62. Matzinger P (1994) Tolerance, danger, and the extended family. Annu Rev Immunol 12: 991-1045.
63. Jerne NK (1974) Towards a network theory of the immune system. Ann Immunol (Paris) 125C: 373-389.
64. Carrington M, Nelson GW, Martin MP, Kissner T, Vlahov D, et al. (1999) HLA and HIV-1: heterozygote advantage and B35-Cw04 disadvantage. Science 283: 1748-1752.
65. Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, et al. (2009) NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61: 1-13.
66. Larsen JE, Lund O, Nielsen M (2006) Improved method for predicting linear Bcell epitopes. Immunome Res 2.
67. Haste Andersen P, Nielsen M, Lund O (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 15: 2558-2567.
68. Lin HH, Zhang GL, Tongchusak S, Reinherz EL, Brusic V (2008) Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics 9 Suppl 12: S22.
69. 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.
70. Tang ST, Wang M, Lamberth K, Harndahl M, Dziegiel MH, et al. (2008) Mhci- restricted epitopes conserved among variola and other related orthopoxviruses are recognized by t cells 30 years after vaccination. Arch Virol 153: 1833-44.
71. Sette A, Sidney J, Bui HH, del Guercio MF, Alexander J, et al. (2005) Characterization of the peptide-binding specificity of mamu-a11 results in the identification of siv-derived epitopes and interspecies cross-reactivity. Immunogenetics 57: 53-68.
72. Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, et al. (2003) Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci 12: 1007-1017.
73. Rapin N, Hoof I, Lund O, Nielsen M (2008) MHC motif viewer. Immunogenetics.
74. Miyazawa S, Jernigan RL (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256: 623-644.
75. Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, et al. (2003) Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 62: 378-384.
76. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402.
77. Yewdell JW, Bennink JR (1999) Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu Rev Immunol 17: 51-88.
78. Reche PA, Zhang H, Glutting JP, Reinherz EL (2005) Epimhc: a curated database of mhc-binding peptides for customized computational vaccinology. Bioinformatics 21: 2140-2141.
79. Brusic V, Rudy G, Harrison LC (1994) MHCPEP: a database of MHC-binding peptides. Nucleic Acids Res 22: 3663-3665.
80. Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, et al. (2008) Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol 4: e1000107.
81. Bian H, Hammer J (2004) Discovery of promiscuous HLA-II-restricted T cell epitopes with TEPITOPE. Methods 34: 468-75.
82. Pellequer JL, Westhof E, Van Regenmortel MH (1993) Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol Lett 36: 83-99.
83. Parker JM, Guo D, Hodges RS (1986) New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 25: 5425-5432.
84. Miyazawa S, Jernigan RL (2000) Identifying sequence-structure pairs undetected by sequence alignments. Protein Eng 13: 459-475.
85. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100.