Abstract
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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Flower DR (2007) Immunoinformatics and the in silico prediction of immunogenicity. An introduction. Methods Mol Biol 409:1–15
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):211–250
Lefranc MP (2011) IMGT, the international ImMunoGeneTics information system. Cold Spring Harb Protoc 2011(6):595–603
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 issue
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):101–111
Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG (2011) The IMGT/HLA database. Nucleic Acids Res 39:D1171–D1176, Database issue
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 issue
Retter I, Althaus HH, Munch R, Muller W (2005) VBASE2, an integrative V gene database. Nucleic Acids Res 33:D671–D674, Database issue
Robinson J, Marsh SG (2007) IPD: the immuno polymorphism database. Methods Mol Biol 409:61–74
Robinson J, Mistry K, McWilliam H, Lopez R, Marsh SG (2010) IPD–the immuno polymorphism database. Nucleic Acids Res 38:D863–D869, Database issue
Robinson J, Waller MJ, Fail SC, Marsh SG (2006) The IMGT/HLA and IPD databases. Hum Mutat 27(12):1192–1199
Robinson J, Waller MJ, Stoehr P, Marsh SG (2005) IPD–the immuno polymorphism database. Nucleic Acids Res 33:D523–D526, Database issue
Schuler MM, Nastke MD, Stevanovikc S (2007) SYFPEITHI: database for searching and T-cell epitope prediction. Methods Mol Biol 409:75–93
Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50(3–4):213–219
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):813–822
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):4516–4525
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):3913–3924
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):32426–32434
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):7736–7743
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):620–631
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):163–175
Brusic V, Rudy G, Harrison LC (1998) MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res 26(1):368–371
Brusic V, Rudy G, Kyne AP, Harrison LC (1997) MHCPEP, a database of MHC-binding peptides: update 1996. Nucleic Acids Res 25(1):269–271
Brusic V, Rudy G, Kyne AP, Harrison LC (1996) MHCPEP–a database of MHC-binding peptides: update 1995. Nucleic Acids Res 24(1):242–244
Brusic V, Rudy G, Harrison LC (1994) MHCPEP: a database of MHC-binding peptides. Nucleic Acids Res 22(17):3663–3665
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 :947–951
Schonbach C, Koh JLY, Flower DR, Brusic V (2005) An update on the functional molecular immunology (FIMM) database. Appl Bioinformatics 4(1):25–31
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):226–229
Schonbach C, Koh JL, Sheng X, Wong L, Brusic V (2000) FIMM, a database of functional molecular immunology. Nucleic Acids Res 28(1):222–224
Reche PA, Zhang H, Glutting JP, Reinherz EL (2005) EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology. Bioinformatics 21(9):2140–2141
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):12–19
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):1192–1193
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):111–114
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):309–310
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 issue
Middleton D, Menchaca L, Rood H, Komerofsky R (2003) New allele frequency database: http://www.allelefrequencies.net. Tissue Antigens 61(5):403–407
Saha S, Raghava GP (2007) Searching and mapping of B-cell epitopes in Bcipep database. Methods Mol Biol 409:113–124
Saha S, Bhasin M, Raghava GP (2005) Bcipep: a database of B-cell epitopes. BMC Genomics 6:79
Huang J, Honda W (2006) CED: a conformational epitope database. BMC Immunol 7:7
Singh MK, Srivastava S, Raghava GP, Varshney GC (2006) HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies. Bioinformatics 22(2):253–255
Kuiken C, Korber B, Shafer RW (2003) HIV sequence databases. AIDS Rev 5(1):52–61
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):217–225
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):4
Lata S, Bhasin M, Raghava GP (2009) MHCBN 4.0: a database of MHC/TAP binding peptides and T-cell epitopes. BMC Res Notes 2:61
Bhasin M, Singh H, Raghava GP (2003) MHCBN: a comprehensive database of MHC binding and non-binding peptides. Bioinformatics 19(5):665–666
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):e91
Sette A (2004) The immune epitope database and analysis resource: from vision to blueprint. Genome Inform 15(2):299
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 issue
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 issue
Wassenaar TM, Gaastra W (2001) Bacterial virulence: can we draw the line? FEMS Microbiol Lett 201(1):1–7
Ansari HR, Flower DR, Raghava GPS (2010) AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res 38:D847–D853
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 issue
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):46–59
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):144–151
Allred DR, Barbet AF, Barry JD, Deitsch KW (2009) varDB: common ground for a shifting landscape. Trends Parasitol 25(6):249–252
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):2564–2565
Tongchusak S, Chaiyaroj SC, Veeramani A, Koh JLY, Brusic V (2005) CandiVF—Candida albicans virulence factor database. Int J Pep Res Ther 11(4):271–277
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 issue
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 issue
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–D464
Kamble S, Bharmal M (2009) Incremental direct expenditure of treating asthma in the United States. J Asthma 46(1):73–80
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):4830–4837
Ivanciuc O, Schein CH, Braun W (2003) SDAP: database and computational tools for allergenic proteins. Nucleic Acids Res 31(1):359–362
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 127:44–49
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 123:32–36
Mari A, Scala E (2006) Allergome: a unifying platform. Arb Paul Ehrlich Inst Bundesamt Sera Impfstoffe Frankf AM 95:29–39, discussion 39–40
Chardin H, Peltre G (2005) Allergome: the characterization of allergens based on a 2D gel electrophoresis approach. Expert Rev Proteomics 2(5):757–765
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this chapter
Cite this chapter
Ansari, H.R., Flower, D.R., Raghava, G.P.S. (2013). On the Development of Vaccine Antigen Databases: Progress, Opportunity, and Challenge. In: Flower, D., Perrie, Y. (eds) Immunomic Discovery of Adjuvants and Candidate Subunit Vaccines. Immunomics Reviews:, vol 5. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-5070-2_7
Download citation
DOI: https://doi.org/10.1007/978-1-4614-5070-2_7
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-5069-6
Online ISBN: 978-1-4614-5070-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)