On the Development of Vaccine Antigen Databases: Progress, Opportunity, and Challenge

  • Hifzur Rahman Ansari
  • Darren R. Flower
  • Gajendra P. S. Raghava
Part of the Immunomics Reviews: book series (IMMUN, volume 5)


The accumulation of relevant and appropriate data is the essential preliminary to any successful informatics-based exercise in prediction. Without quality data, meaningful prediction is impossible. This is as true in immunobiology as it is in any other branch of the natural sciences. Within the context of vaccine discovery, the accumulation, storage, and retrieval of immunological data within publically accessible repositories, typically web-based databases, is of overwhelming operational importance. Specifically, and with the special reference to the discovery of subunit vaccines, this chapter explores the current state and status of immunological databases focussed on immunogenic proteins, primarily pathogen antigens and environmental allergens. It sets this exploration firmly into context by simultaneously scoping out the rather more mature backdrop provided by epitope-orientated database systems.


Major Histocompatibility Complex Allergenic Protein Major Histocompatibility Complex Allele Major Histocompatibility Complex Binding Primary Scientific Literature 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Flower DR (2007) Immunoinformatics and the in silico prediction of immunogenicity. An introduction. Methods Mol Biol 409:1–15PubMedCrossRefGoogle Scholar
  2. 2.
    Wu TT, Kabat EA (1970) An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J Exp Med 132(2):211–250PubMedCrossRefGoogle Scholar
  3. 3.
    Lefranc MP (2011) IMGT, the international ImMunoGeneTics information system. Cold Spring Harb Protoc 2011(6):595–603PubMedGoogle Scholar
  4. 4.
    Lefranc MP, Giudicelli V, Ginestoux C, Jabado-Michaloud J, Folch G, Bellahcene F, Wu Y, Gemrot E, Brochet X, Lane J et al (2009) IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res 37:D1006–D1012, Database issuePubMedCrossRefGoogle Scholar
  5. 5.
    Lefranc MP (2008) IMGT, the International ImMunoGeneTics Information System for Immunoinformatics: methods for querying IMGT databases, tools, and web resources in the context of immunoinformatics. Mol Biotechnol 40(1):101–111PubMedCrossRefGoogle Scholar
  6. 6.
    Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG (2011) The IMGT/HLA database. Nucleic Acids Res 39:D1171–D1176, Database issuePubMedCrossRefGoogle Scholar
  7. 7.
    Robinson J, Waller MJ, Fail SC, McWilliam H, Lopez R, Parham P, Marsh SG (2009) The IMGT/HLA database. Nucleic Acids Res 37:D1013–D1017, Database issuePubMedCrossRefGoogle Scholar
  8. 8.
    Retter I, Althaus HH, Munch R, Muller W (2005) VBASE2, an integrative V gene database. Nucleic Acids Res 33:D671–D674, Database issuePubMedCrossRefGoogle Scholar
  9. 9.
    Robinson J, Marsh SG (2007) IPD: the immuno polymorphism database. Methods Mol Biol 409:61–74PubMedCrossRefGoogle Scholar
  10. 10.
    Robinson J, Mistry K, McWilliam H, Lopez R, Marsh SG (2010) IPD–the immuno polymorphism database. Nucleic Acids Res 38:D863–D869, Database issuePubMedCrossRefGoogle Scholar
  11. 11.
    Robinson J, Waller MJ, Fail SC, Marsh SG (2006) The IMGT/HLA and IPD databases. Hum Mutat 27(12):1192–1199PubMedCrossRefGoogle Scholar
  12. 12.
    Robinson J, Waller MJ, Stoehr P, Marsh SG (2005) IPD–the immuno polymorphism database. Nucleic Acids Res 33:D523–D526, Database issuePubMedCrossRefGoogle Scholar
  13. 13.
    Schuler MM, Nastke MD, Stevanovikc S (2007) SYFPEITHI: database for searching and T-cell epitope prediction. Methods Mol Biol 409:75–93PubMedCrossRefGoogle Scholar
  14. 14.
    Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50(3–4):213–219PubMedCrossRefGoogle Scholar
  15. 15.
    Sette A, Sidney J, del Guercio MF, Southwood S, Ruppert J, Dahlberg C, Grey HM, Kubo RT (1994) Peptide binding to the most frequent HLA-A class I alleles measured by quantitative molecular binding assays. Mol Immunol 31(11):813–822PubMedCrossRefGoogle Scholar
  16. 16.
    Sidney J, Oseroff C, del Guercio MF, Southwood S, Krieger JI, Ishioka GY, Sakaguchi K, Appella E, Sette A (1994) Definition of a DQ3.1-specific binding motif. J Immunol 152(9):4516–4525PubMedGoogle Scholar
  17. 17.
    Kubo RT, Sette A, Grey HM, Appella E, Sakaguchi K, Zhu NZ, Arnott D, Sherman N, Shabanowitz J, Michel H et al (1994) Definition of specific peptide motifs for four major HLA-A alleles. J Immunol 152(8):3913–3924PubMedGoogle Scholar
  18. 18.
    DiBrino M, Parker KC, Margulies DH, Shiloach J, Turner RV, Biddison WE, Coligan JE (1994) The HLA-B14 peptide binding site can accommodate peptides with different combinations of anchor residues. J Biol Chem 269(51):32426–32434PubMedGoogle Scholar
  19. 19.
    Parker KC, Biddison WE, Coligan JE (1994) Pocket mutations of HLA-B27 show that anchor residues act cumulatively to stabilize peptide binding. Biochemistry 33(24):7736–7743PubMedCrossRefGoogle Scholar
  20. 20.
    DiBrino M, Parker KC, Shiloach J, Turner RV, Tsuchida T, Garfield M, Biddison WE, Coligan JE (1994) Endogenous peptides with distinct amino acid anchor residue motifs bind to HLA-A1 and HLA-B8. J Immunol 152(2):620–631PubMedGoogle Scholar
  21. 21.
    Parker KC, Bednarek MA, Coligan JE (1994) Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol 152(1):163–175PubMedGoogle Scholar
  22. 22.
    Brusic V, Rudy G, Harrison LC (1998) MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res 26(1):368–371PubMedCrossRefGoogle Scholar
  23. 23.
    Brusic V, Rudy G, Kyne AP, Harrison LC (1997) MHCPEP, a database of MHC-binding peptides: update 1996. Nucleic Acids Res 25(1):269–271PubMedCrossRefGoogle Scholar
  24. 24.
    Brusic V, Rudy G, Kyne AP, Harrison LC (1996) MHCPEP–a database of MHC-binding peptides: update 1995. Nucleic Acids Res 24(1):242–244PubMedCrossRefGoogle Scholar
  25. 25.
    Brusic V, Rudy G, Harrison LC (1994) MHCPEP: a database of MHC-binding peptides. Nucleic Acids Res 22(17):3663–3665PubMedCrossRefGoogle Scholar
  26. 26.
    Hon L, Abernethy NF, Brusic V, Chai J, Altman RB (1998) MHCWeb: converting a WWW database into a knowledge-based collaborative environment. Proc AMIA Symp :947–951Google Scholar
  27. 27.
    Schonbach C, Koh JLY, Flower DR, Brusic V (2005) An update on the functional molecular immunology (FIMM) database. Appl Bioinformatics 4(1):25–31PubMedCrossRefGoogle Scholar
  28. 28.
    Schonbach C, Koh JLY, Flower DR, Wong L, Brusic V (2002) FIMM, a database of functional molecular immunology: update 2002. Nucleic Acids Res 30(1):226–229PubMedCrossRefGoogle Scholar
  29. 29.
    Schonbach C, Koh JL, Sheng X, Wong L, Brusic V (2000) FIMM, a database of functional molecular immunology. Nucleic Acids Res 28(1):222–224PubMedCrossRefGoogle Scholar
  30. 30.
    Reche PA, Zhang H, Glutting JP, Reinherz EL (2005) EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology. Bioinformatics 21(9):2140–2141PubMedCrossRefGoogle Scholar
  31. 31.
    Sathiamurthy M, Hickman HD, Cavett JW, Zahoor A, Prilliman K, Metcalf S, Fernandez Vina M, Hildebrand WH (2003) Population of the HLA ligand database. Tissue Antigens 61(1):12–19PubMedCrossRefGoogle Scholar
  32. 32.
    Khan JM, Cheruku HR, Tong JC, Ranganathan S (2011) MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures. Bioinformatics 27(8):1192–1193PubMedCrossRefGoogle Scholar
  33. 33.
    Tong JC, Kong L, Tan TW, Ranganathan S (2006) MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions. Appl Bioinformatics 5(2):111–114PubMedCrossRefGoogle Scholar
  34. 34.
    Govindarajan KR, Kangueane P, Tan TW, Ranganathan S (2003) MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. Bioinformatics 19(2):309–310PubMedCrossRefGoogle Scholar
  35. 35.
    Gonzalez-Galarza FF, Christmas S, Middleton D, Jones AR (2011) Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res 39:D913–D919, Database issuePubMedCrossRefGoogle Scholar
  36. 36.
    Middleton D, Menchaca L, Rood H, Komerofsky R (2003) New allele frequency database: Tissue Antigens 61(5):403–407PubMedCrossRefGoogle Scholar
  37. 37.
    Saha S, Raghava GP (2007) Searching and mapping of B-cell epitopes in Bcipep database. Methods Mol Biol 409:113–124PubMedCrossRefGoogle Scholar
  38. 38.
    Saha S, Bhasin M, Raghava GP (2005) Bcipep: a database of B-cell epitopes. BMC Genomics 6:79PubMedCrossRefGoogle Scholar
  39. 39.
    Huang J, Honda W (2006) CED: a conformational epitope database. BMC Immunol 7:7PubMedCrossRefGoogle Scholar
  40. 40.
    Singh MK, Srivastava S, Raghava GP, Varshney GC (2006) HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies. Bioinformatics 22(2):253–255PubMedCrossRefGoogle Scholar
  41. 41.
    Kuiken C, Korber B, Shafer RW (2003) HIV sequence databases. AIDS Rev 5(1):52–61PubMedGoogle Scholar
  42. 42.
    Yusim K, Richardson R, Tao N, Dalwani A, Agrawal A, Szinger J, Funkhouser R, Korber B, Kuiken C (2005) Los alamos hepatitis C immunology database. Appl Bioinformatics 4(4):217–225PubMedCrossRefGoogle Scholar
  43. 43.
    Toseland CP, Clayton DJ, McSparron H, Hemsley SL, Blythe MJ, Paine K, Doytchinova IA, Guan P, Hattotuwagama CK, Flower DR (2005) AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res 1(1):4PubMedCrossRefGoogle Scholar
  44. 44.
    Lata S, Bhasin M, Raghava GP (2009) MHCBN 4.0: a database of MHC/TAP binding peptides and T-cell epitopes. BMC Res Notes 2:61PubMedCrossRefGoogle Scholar
  45. 45.
    Bhasin M, Singh H, Raghava GP (2003) MHCBN: a comprehensive database of MHC binding and non-binding peptides. Bioinformatics 19(5):665–666PubMedCrossRefGoogle Scholar
  46. 46.
    Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O et al (2005) The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol 3(3):e91PubMedCrossRefGoogle Scholar
  47. 47.
    Sette A (2004) The immune epitope database and analysis resource: from vision to blueprint. Genome Inform 15(2):299PubMedGoogle Scholar
  48. 48.
    Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B (2010) The immune epitope database 2.0. Nucleic Acids Res 38:D854–D862, Database issuePubMedCrossRefGoogle Scholar
  49. 49.
    Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J et al (2008) Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res 36:W513–W518, Web Server issuePubMedCrossRefGoogle Scholar
  50. 50.
    Wassenaar TM, Gaastra W (2001) Bacterial virulence: can we draw the line? FEMS Microbiol Lett 201(1):1–7PubMedCrossRefGoogle Scholar
  51. 51.
    Ansari HR, Flower DR, Raghava GPS (2010) AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res 38:D847–D853PubMedCrossRefGoogle Scholar
  52. 52.
    Xiang Z, Todd T, Ku KP, Kovacic BL, Larson CB, Chen F, Hodges AP, Tian Y, Olenzek EA, Zhao B et al (2008) VIOLIN: vaccine investigation and online information network. Nucleic Acids Res 36:D923–D928, Database issuePubMedCrossRefGoogle Scholar
  53. 53.
    Hayes CN, Diez D, Joannin N, Kanehisa M, Wahlgren M, Wheelock CE, Goto S (2009) Tools for investigating mechanisms of antigenic variation: new extensions to varDB. Genome Inform 23(1):46–59PubMedCrossRefGoogle Scholar
  54. 54.
    Diez D, Hayes N, Joannin N, Normark J, Kanehisa M, Wahlgren M, Wheelock CE, Goto S (2010) varDB: a database of antigenic variant sequences–current status and future prospects. Acta Trop 114(3):144–151PubMedCrossRefGoogle Scholar
  55. 55.
    Allred DR, Barbet AF, Barry JD, Deitsch KW (2009) varDB: common ground for a shifting landscape. Trends Parasitol 25(6):249–252PubMedCrossRefGoogle Scholar
  56. 56.
    Hayes CN, Diez D, Joannin N, Honda W, Kanehisa M, Wahlgren M, Wheelock CE, Goto S (2008) varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. Bioinformatics 24(21):2564–2565PubMedCrossRefGoogle Scholar
  57. 57.
    Tongchusak S, Chaiyaroj SC, Veeramani A, Koh JLY, Brusic V (2005) CandiVF—Candida albicans virulence factor database. Int J Pep Res Ther 11(4):271–277CrossRefGoogle Scholar
  58. 58.
    Yang J, Chen L, Sun L, Yu J, Jin Q (2008) VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. Nucleic Acids Res 36:D539–D542, Database issuePubMedCrossRefGoogle Scholar
  59. 59.
    Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33:D325–D328, Database issuePubMedCrossRefGoogle Scholar
  60. 60.
    Winnenburg R, Baldwin TK, Urban M, Rawlings C, Kohler J, Hammond-Kosack KE (2006) PHI-base: a new database for pathogen host interactions. Nucleic Acids Res 34:D459–D464PubMedCrossRefGoogle Scholar
  61. 61.
    Kamble S, Bharmal M (2009) Incremental direct expenditure of treating asthma in the United States. J Asthma 46(1):73–80PubMedCrossRefGoogle Scholar
  62. 62.
    Ivanciuc O, Mathura V, Midoro-Horiuti T, Braun W, Goldblum RM, Schein CH (2003) Detecting potential IgE-reactive sites on food proteins using a sequence and structure database, SDAP-food. J Agric Food Chem 51(16):4830–4837PubMedCrossRefGoogle Scholar
  63. 63.
    Ivanciuc O, Schein CH, Braun W (2003) SDAP: database and computational tools for allergenic proteins. Nucleic Acids Res 31(1):359–362PubMedCrossRefGoogle Scholar
  64. 64.
    Nakamura R, Teshima R (2009) Major revision of the allergen database for food safety (ADFS) and validation of the motif-based allergenicity prediction tool. Kokuritsu Iyakuhin Shokuhin Eisei Kenkyusho Hokoku 127:44–49PubMedGoogle Scholar
  65. 65.
    Nakamura R, Teshima R, Takagi K, Sawada J (2005) Development of Allergen Database for Food Safety (ADFS): an integrated database to search allergens and predict allergenicity. Kokuritsu Iyakuhin Shokuhin Eisei Kenkyusho Hokoku 123:32–36PubMedGoogle Scholar
  66. 66.
    Mari A, Scala E (2006) Allergome: a unifying platform. Arb Paul Ehrlich Inst Bundesamt Sera Impfstoffe Frankf AM 95:29–39, discussion 39–40Google Scholar
  67. 67.
    Chardin H, Peltre G (2005) Allergome: the characterization of allergens based on a 2D gel electrophoresis approach. Expert Rev Proteomics 2(5):757–765PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Hifzur Rahman Ansari
    • 1
  • Darren R. Flower
    • 2
  • Gajendra P. S. Raghava
    • 1
  1. 1.Bioinformatics Centre, Institute of Microbial TechnologyChandigarhIndia
  2. 2.School of Life and Health SciencesAston UniversityBirminghamUK

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