Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties

Molecular Immunology

Volumn 44, Issue 4, 2007, Pages 514-520

  Cui, Juan ^a   Han, Lian Yi ^a   Li, Hu ^a   Ung, Choong Yong ^a   Tang, Zhi Qun ^a   Zheng, Chan Juan ^a   Cao, Zhi Wei ^b   Chen, Yu Zong ^a,b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

Allergen; Immunology; Statistical learning method; Support vector machine

Indexed keywords

ALLERGEN;

ALLERGENICITY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PREDICTION; DATA BASE; ENZYME INHIBITION; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS;

ALLERGENS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PREDICTIVE VALUE OF TESTS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN;

EID: 33748199236     PISSN: 01615890     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molimm.2006.02.010     Document Type: Article

References (43)

1. Altschul S., Madden T., Schaffer A., Zhang J., Zhang Z., Miller W., and Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25 (1997) 3389-3402
2. Baldi P., Brunak S., Chauvin Y., Andersen C.A., and Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16 (2000) 412-424
3. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S., Griffiths-Jones S., Howe K., Marshall M., and Sonnhammer E. The Pfam protein families database. Nucl. Acids Res. 30 (2002) 276-280
4. Bochner B.S., and Busse W.W. Advances in mechanisms of allergy. J. Allergy Clin. Immunol. 113 (2004) 868-875
5. Bredehorst R., and David K. What establishes a protein as an allergen?. J. Chromatogr. B, Biomed. Sci. Appl. 756 (2001) 33-40
6. Breiteneder H., and Clare Mills E.N. Plant food allergens-structural and functional aspects of allergenicity. Biotechnol. Adv. 23 (2005) 395-399
7. Breiteneder H., and Ebner C. Molecular and biochemical classification of plant-derived food allergens. J. Allergy Clin. Immunol. 106 (2000) 27-36
8. Breiteneder H., and Ebner C. Atopic allergens of plant foods. Curr. Opin. Allergy Clin. Immunol. 1 (2001) 261-267
9. Breiteneder H., and Mills C. Nonspecific lipid-transfer proteins in plant foods and pollens: an important allergen class. Curr. Opin. Allergy Clin. Immunol. 5 (2005) 275-279
10. Breiteneder H., and Mills E.N. Molecular properties of food allergens. J. Allergy Clin. Immunol. 115 (2005) 14-23 (quiz 24)
11. Brusic V., Petrovsky N., Gendel S., Millot M., Gigonzac O., and Stelman S. Computational tools for the study of allergens. Allergy 58 (2003) 1083-1092
12. Burges C. A tutorial on support vector machines for pattern recognition. Data Min. Knowl. Disc. 2 (1998) 121-167
13. Cai C., Han L., Ji Z., Chen X., and Chen Y. SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence. Nucl. Acids Res. 31 (2003) 3692-3697
14. Cebra J.J., Fuhrman J.A., Griffin P., Rose F.V., Schweitzer P.A., and Zimmerman D. Changes in specific B cells and the dissemination of the primed state in vivo following antigenic stimulation by different mucosal routes. Ann. Allergy 53 (1984) 541-549
15. Cookson W. The immunogenetics of asthma and eczema: a new focus on the epithelium. Nat. Rev. Immunol. 4 (2004) 978-988
16. Davis P.J., Smales C.M., and James D.C. How can thermal processing modify the antigenicity of proteins?. Allergy 56 Suppl. 67 (2001) 56-60
17. Fiers M.W., Kleter G.A., Nijland H., Peijnenburg A.A., Nap J.P., and van Ham R.C. Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines. BMC Bioinform. 5 (2004) 133
18. Gasteiger E., Jung E., and Bairoch A. SWISS-PROT: connecting biomolecular knowledge via a protein database. Curr. Issues Mol. Biol. 3 (2001) 47-55
19. Gould H., Sutton B., Beavil A., Beavil R., McCloskey N., Coker H., Fear D., and Smurthwaite L. The biology of IGE and the basis of allergic disease. Ann. Rev. Immunol. 21 (2003) 579-628
20. Han L., Cai C., Ji Z., Cao Z., Cui J., and Chen Y. Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach. Nucl. Acids Res. 32 (2004) 6437-6444
21. Han L., Cai C., Ji Z., and Chen Y. Prediction of functional class of novel viral proteins by a statistical learning method irrespective of sequence similarity. Virology 331 (2005) 136-143
22. Han L., Cai C., Lo S., Chung M., and Chen Y. Prediction of RNA-binding proteins from primary sequence by a support vector machine approach. RNA 10 (2004) 355-368
23. Hileman R., Silvanovich A., Goodman R., Rice E., Holleschak G., Astwood J., and Hefle S. Bioinformatic methods for allergenicity assessment using a comprehensive allergen database. Int. Arch. Allergy Immunol. 128 (2002) 280-291
24. Huby R.D., Dearman R.J., and Kimber I. Why are some proteins allergens?. Toxicol. Sci. 55 (2000) 235-246
25. Ivanciuc O., Mathura V., Midoro-Horiuti T., Braun W., Goldblum R., and Schein C. Detecting potential IgE-reactive sites on food proteins using a sequence and structure database, SDAP-food. J. Agric. Food Chem. 51 (2003) 4830-4837
26. Kleter G., and Peijnenburg A. 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 (2002) 8
27. Lack G. New developments in food allergy: old questions remain. J. Allergy Clin. Immunol. 114 (2004) 127-130
28. Li K.B., Issac P., and Krishnan A. Predicting allergenic proteins using wavelet transform. Bioinformatics 20 (2004) 2572-2578
29. Malandain H. Basic immunology, allergen prediction, and bioinformatics. Allergy 59 (2004) 1011-1012
30. Mills E.N., Jenkins J.A., Alcocer M.J., and Shewry P.R. Structural, biological, and evolutionary relationships of plant food allergens sensitizing via the gastrointestinal tract. Crit. Rev. Food Sci. Nutr. 44 (2004) 379-407
31. Ono S. Molecular genetics of allergic diseases. Ann. Rev. Immunol. 18 (2000) 347-366
32. Provost F., Fawcett T., and Kohavi R. The case against accuracy estimation for comparing induction algorithms. Proceedings of the 15th International Conference on Machine Learning. Morgan Kaufmann, San Francisco, CA (1998) 445-453
33. Sampson H. Update on food allergy. J. Allergy Clin. Immunol. 113 (2004) 805-819
34. Sicherer S., Munoz-Furlong A., and Sampson H. Prevalence of seafood allergy in the United States determined by a random telephone survey. J. Allergy Clin. Immunol. 114 (2004) 159-165
35. Soeria-Atmadja D., Zorzet A., Gustafsson M., and Hammerling U. Statistical evaluation of local alignment features predicting allergenicity using supervised classification algorithms. Int. Arch. Allergy Immunol. 133 (2004) 101-112
36. Stadler M.B., and Stadler B.M. Allergenicity prediction by protein sequence. FASEB J. 17 (2003) 1141-1143
37. Stewart G.T. Allergy to penicillin and related antibiotics: antigenic and immunochemical mechanism. Annu. Rev. Pharmacol. 13 (1973) 309-324
38. Sutton B., and Gould H. The human IgE network. Nature 366 (1993) 421-428
39. Todd A., Orengo C., and Thornton J. Plasticity of enzyme active sites. Trends Biochem. Sci. 27 (2002) 419-426
40. van Wijk F., Nierkens S., Hassing I., Feijen M., Koppelman S.J., de Jong G.A., Pieters R., and Knippels L.M. The effect of the food matrix on in vivo immune responses to purified peanut allergens. Toxicol. Sci. 86 (2005) 333-341
41. Venge J., Lampinen M., Hakansson L., Rak S., and Venge P. Identification of IL-5 and RANTES as the major eosinophil chemoattractants in the asthmatic lung. J. Allergy Clin. Immunol. 97 (1996) 1110-1115
42. Wal J.M. Structure and function of milk allergens. Allergy 56 Suppl. 67 (2001) 35-38
43. Zorzet A., Gustafsson M., and Hammerling U. Prediction of food protein allergenicity: a bioinformatic learning systems approach. In Silico Biol. 2 (2002) 525-534