EVALLER: A web server for in silico assessment of potential protein allergenicity

Nucleic Acids Research

Volumn 35, Issue SUPPL.2, 2007, Pages

  Barrio, Alvaro Martinez ^a,e   Soeria Atmadja, Daniel ^b,d   Nistér, Anders ^a   Gustafsson, Mats G ^c,d   Hammerling, Ulf ^b   Bongcam Rudloff, Erik ^a,e  

^a UPPSALA UNIVERSITY   (Sweden)

^b NATIONAL FOOD ADMINISTRATION   (Sweden)

^c UPPSALA UNIVERSITY   (Sweden)

^d UPPSALA UNIVERSITY HOSPITAL   (Sweden)

^e SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALLERGEN; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; CROSS REACTION; HUMAN; IMMUNOLOGY; INTERNET; METHODOLOGY; MOLECULAR GENETICS; PROTEIN DATABASE; SEQUENCE ANALYSIS;

ALGORITHMS; ALLERGENS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; CROSS REACTIONS; DATABASES, PROTEIN; HUMANS; INTERNET; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 34547567978     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm370     Document Type: Article

References (46)

1. Hjern, A. (2006) Chapter 5.8: major public health problems-allergic disorders. Scand J. Public Health Suppl., 67, 125-131.
2. Johansson, S.G., Bieber, T., Dahl, R., Friedmann, P.S., Lanier, B.Q., Lockey, R.F., Motala, C., Ortega Martell, J.A., Platts-Mills, T.A. et al. (2004) Revised nomenclature for allergy for global use: Report of the Nomenclature Review Committee of the World Allergy Organization, October 2003. J. Allergy Clin. Immunol., 113, 832-836.
3. Ferreira, F., Hawranek, T., Gruber, P., Wopfner, N. and Mari, A. (2004) Allergic cross-reactivity: from gene to the clinic. Allergy, 59, 243-267.
4. Chaplin, D.D. (2006) 1. Overview of the human immune response. J. Allergy Clin. Immunol., 117, S430-S435.
5. Romagnani, S. (2006) Regulatory T cells: which role in the pathogenesis and treatment of allergic disorders? Allergy, 61, 3-14.
6. Aalberse, R.C. and Platts-Mills, T.A. (2004) How do we avoid developing allergy: modifications of the TH2 response from a B-cell perspective. J. Allergy Clin. Immunol., 113, 983-986.
7. Woodfolk, J.A. (2007) T-cell responses to allergens. J. Allergy Clin. Immunol., 119, 280-294.
8. Platts-Mills, T.A. (2001) The role of immunoglobulin E in allergy and asthma. Am. J. Respir. Crit. Care Med., 164, S1-S5.
9. Kay, A.B. (2001) Allergy and allergic diseases. Second of two parts. New Engl. J. Med., 344, 109-113.
10. Gould, H.J., Sutton, B.J., Beavil, A.J., Beavil, R.L., McCloskey, N., Coker, H.A., Fear, D. and Smurthwaite, L. (2003) The biology of IGE and the basis of allergic disease. Annu. Rev. Immunol., 21, 579-628.
11. Aalberse, R.C., Akkerdaas, J. and van Ree, R. (2001) Cross-reactivity of IgE antibodies to allergens. Allergy, 56, 478-490.
12. Yagami, T. (2002) Allergies to cross-reactive plant proteins. Latex-fruit syndrome is comparable with pollen-food allergy syndrome. Int. Arch. Allergy Immunol., 128, 271-279.
13. Radauer, C., Willerroider, M., Fuchs, H., Hoffmann-Sommergruber, K., Thalhamer, J., Ferreira, F., Scheiner, O. and Breiteneder, H. (2006) Cross-reactive and species-specific immuno-globulin E epitopes of plant profilins: an experimental and structure-based analysis. Clin. Exp. Allergy, 36, 920-929.
14. Burastero, S.E., Paolucci, C., Breda, D., Longhi, R., Silvestri, M., Hammer, J., Protti, M.P. and Rossi, G.A. (2004) T-cell receptor-mediated cross-allergenicity. Int. Arch. Allergy Immunol., 135, 296-305.
15. Bannon, G.A. and Ogawa, T. (2006) Evaluation of available IgE-binding epitope data and its utility in bioinformatics. Mol. Nutr. Food Res, 50, 638-644.
16. Bohle, B. (2006) T-cell epitopes of food allergens. Clin. Rev. Allergy Immunol., 30, 97-108.
17. Blanco, C. (2003) Latex-fruit syndrome. Curr. Allergy Asthma. Rep., 3, 47-53.
18. Egger, M., Mutschlechner, S., Wopfner, N., Gadermaier, G., Briza, P. and Ferreira, F. (2006) Pollen-food syndromes associated with weed pollinosis: an update from the molecular point of view. Allergy, 61, 461-476.
19. Bowyer, P., Fraczek, M. and Denning, D.W. (2006) Comparative genomics of fungal allergens and epitopes shows widespread distribution of closely related allergen and epitope orthologues. BMC Genomics, 7, 251.
20. Breiteneder, H. and Mills, C. (2006) Structural bioinformatic approaches to understand cross-reactivity. Mol. Nutr. Food Res., 50, 628-632.
21. Aalberse, R.C. (2000) Structural biology of allergens. J. Allergy Clin. Immunol., 106, 228-238.
22. Mills, E.N.C., Madsen, C., Shewry, P.R. and Wichers, H.J. (2003) Food allergens of plant origin-their molecular and evolutionary relationships. Trends Food Sci. Technol., 14, 145-156.
23. Metcalfe, D.D., Astwood, J.D., Townsend, R., Sampson, H.A., Taylor, S.L. and Fuchs, R.L. (1996) Assessment of the allergenic potential of foods derived from genetically engineered crop plants. Crit. Rev. Food Sci. Nutr., 36(Suppl), S165-S186
24. FAO/WHO. (2001) Evaluation of allergenicity of genetically modified foods. Joint FAO/WHO Expert Consultation on Allergenicity of Foods Derived from Biotechnology, Rome, Italy.
25. Codex. (2003) Codex Alimentarius Commission. Report of the fourth session of the Codex ad hoc intergovernmental task force on foods derived from biotechnology (ALINORM 03/34A). Codex Alimentarius Commission, Yokohama.
26. EFSA. (2004) Guidance document of the Scientific Panel on Genetically Modified Organisms for the risk assessment of genetically modified plants and derived food and feed. EFSA J., 99, 1-94.
27. Zorzet, A., Gustafsson, M. and Hammerling, U. (2002) Prediction of food protein allergenicity: a bioinformatic learning systems approach. In Silico Biol., 2, 525-534.
28. Soeria-Atmadja, D., Zorzet, A., Gustafsson, M.G. and Hammerling, U. (2004) Statistical evaluation of local alignment features predicting allergenicity using supervised classification algorithms. Int. Arch. Allergy Immunol., 133, 101-112.
29. Bjorklund, A.K., Soeria-Atmadja, D., Zorzet, A., Hammerling, U. and Gustafsson, M.G. (2005) Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins. Bioinformatics, 21, 39-50.
30. Soeria-Atmadja, D., Lundell, T., Gustafsson, M.G. and Hammerling, U. (2006) Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning. Nucleic Acids Res., 34, 3779-3793.
31. Saha, S. and Raghava, G.P. (2006) AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res., 34, W202-W209.
32. Cui, J., Han, L.Y., Li, H., Ung, C.Y., Tang, Z.Q., Zheng, C.J., Cao, Z.W. and Chen, Y.Z. (2007) Computer prediction of allergen proteins from sequence-derived protein structural and physico-chemical properties. Mol. Immunol., 44, 514-520.
33. Ivanciuc, O., Schein, C.H. and Braun, W. (2003) SDAP: database and computational tools for allergenic proteins. Nucleic Acids Res., 31, 359-362.
34. Fiers, M.W., Kleter, G.A., Nijland, H., Peijnenburg, A.A., Nap, J.P. and van Ham, R.C. (2004) Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines. BMC Bioinformatics, 5, 133.
35. Riaz, T., Hor, H.L., Krishnan, A., Tang, F. and Li, K.B. (2005) WebAllergen: a web server for predicting allergenic proteins. Bioinformatics, 21, 2570-2571.
36. Valenta, R., Hayek, B., Seiberler, S., Bugajska-Schretter, A., Niederberger, V., Twardosz, A., Natter, S., Vangelista, L., Pastore, A. et al. (1998) Calcium-binding allergens: from plants to man. Int. Arch. Allergy Immunol., 117, 160-166.
37. Radauer, C. and Breiteneder, H. (2006) Pollen allergens are restricted to few protein families and show distinct patterns of species distribution. J. Allergy Clin. Immunol., 117, 141-147.
38. Arrieta, I., del Barrio, M., Vidarte, L., del Pozo, V., Pastor, C., Gonzalez-Cabrero, J., Cardaba, B., Rojo, M., Minguez, A. et al. (2000) Molecular cloning and characterization of an IgE-reactive protein from Anisakis simplex: Ani s 1. Mol. Biochem. Parasitol., 107, 263-268.
39. Ledesma, A., Barderas, R., Westritschnig, K., Quiralte, J., Pascual, C.Y., Valenta, R., Villalba, M. and Rodriguez, R. (2006) A comparative analysis of the cross-reactivity in the polcalcin family including Syr v 3, a new member from lilac pollen. Allergy, 61, 477-484.
40. Thomas, K., Aalbers, M., Bannon, G.A., Bartels, M., Dearman, R.J., Esdaile, D.J., Fu, T.J., Glatt, C.M., Hadfield, N. et al. (2004) A multi-laboratory evaluation of a common in vitro pepsin digestion assay protocol used in assessing the safety of novel proteins. Regul. Toxicol. Pharmacol., 39, 87-98.
41. Hileman, R.E., Silvanovich, A., Goodman, R.E., Rice, E.A., Holleschak, G., Astwood, J.D. and Hefle, S.L. (2002) Bioinformatic methods for allergenicity assessment using a comprehensive allergen database. Int. Arch. Allergy Immunol., 128, 280-291.
42. Kleter, G.A. and Peijnenburg, A.A. (2002) Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE-binding linear epitopes of allergens. BMC Struct. Biol., 2, 8.
43. Stadler, M.B. and Stadler, B.M. (2003) Allergenicity prediction by protein sequence. FASEB J., 17, 1141-1143.
44. Li, K.B., Issac, P. and Krishnan, A. (2004) Predicting allergenic proteins using wavelet transform. Bioinformatics, 20, 2572-2578.
45. Ivanciuc, O., Schein, C.H. and Braun, W. (2002) Data mining of sequences and 3D structures of allergenic proteins. Bioinformatics, 18, 1358-1364.
46. Schein, C.H., Ivanciuc, O. and Braun, W. (2005) Common physical-chemical properties correlate with similar structure of the IgE epitopes of peanut allergens. J. Agric. Food Chem., 53, 8752-8759.