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Volumn 34, Issue 13, 2006, Pages 3779-3793

Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning

Author keywords

[No Author keywords available]

Indexed keywords

ALLERGEN; PARVALBUMIN; PEPTIDE; PROFILIN; TROPOMYOSIN; PROTEIN;

EID: 33748672467     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl467     Document Type: Article
Times cited : (40)

References (56)
  • 1
    • 0030951698 scopus 로고    scopus 로고
    • The distribution of total and specific serum IgE in the European Community Respiratory Health Survey
    • Burney,P., Malmberg,E., Chinn,S., Jarvis,D., Luczynska,C. and Lai,E. (1997) The distribution of total and specific serum IgE in the European Community Respiratory Health Survey. J. Allergy Clin. Immunol., 99, 314-322.
    • (1997) J. Allergy Clin. Immunol. , vol.99 , pp. 314-322
    • Burney, P.1    Malmberg, E.2    Chinn, S.3    Jarvis, D.4    Luczynska, C.5    Lai, E.6
  • 3
  • 4
    • 0036883552 scopus 로고    scopus 로고
    • Molecular aspects of allergy
    • Miescher,S.M. and Vogel,M. (2002) Molecular aspects of allergy. Mol. Aspects Med., 23, 413-462.
    • (2002) Mol. Aspects Med. , vol.23 , pp. 413-462
    • Miescher, S.M.1    Vogel, M.2
  • 6
    • 0035843316 scopus 로고    scopus 로고
    • Allergy and allergic diseases. Second of two parts
    • Kay,A.B. (2001) Allergy and allergic diseases. Second of two parts. N. Engl. J. Med., 344, 109-113.
    • (2001) N. Engl. J. Med. , vol.344 , pp. 109-113
    • Kay, A.B.1
  • 7
    • 0034995912 scopus 로고    scopus 로고
    • Cross-reactivity of IgE antibodies to allergens
    • Aalberse,R.C., Akkerdaas,J. and van Ree,R. (2001) Cross-reactivity of IgE antibodies to allergens. Allergy, 56, 478-490.
    • (2001) Allergy , vol.56 , pp. 478-490
    • Aalberse, R.C.1    Akkerdaas, J.2    van Ree, R.3
  • 8
    • 0034778245 scopus 로고    scopus 로고
    • Cross-reactivity of plant and animal allergens
    • Weber,R.W. (2001) Cross-reactivity of plant and animal allergens. Clin. Rev. Allergy Immunol., 21, 153-202.
    • (2001) Clin. Rev. Allergy Immunol. , vol.21 , pp. 153-202
    • Weber, R.W.1
  • 9
    • 0036264052 scopus 로고    scopus 로고
    • Current understanding of cross-reactivity of food allergens and pollen
    • Vieths,S., Scheurer,S. and Ballmer-Weber,B. (2002) Current understanding of cross-reactivity of food allergens and pollen. Ann. NY Acad. Sci., 964, 47-68.
    • (2002) Ann. NY Acad. Sci. , vol.964 , pp. 47-68
    • Vieths, S.1    Scheurer, S.2    Ballmer-Weber, B.3
  • 10
    • 0036673739 scopus 로고    scopus 로고
    • Allergies to cross-reactive plant proteins. Latex-fruit syndrome is comparable with pollen-food Allergy syndrome
    • 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.
    • (2002) Int. Arch. Allergy Immunol. , vol.128 , pp. 271-279
    • Yagami, T.1
  • 13
    • 11344255717 scopus 로고    scopus 로고
    • Structural relatedness of plant food allergens with specific reference to cross-reactive allergens: An in silico analysis
    • Jenkins,J.A., Griffiths-Jones,S., Shewry,P.R., Breiteneder,H. and Mills,E.N. (2005) Structural relatedness of plant food allergens with specific reference to cross-reactive allergens: An in silico analysis. J. Allergy Clin. Immunol., 115, 163-170.
    • (2005) J. Allergy Clin. Immunol. , vol.115 , pp. 163-170
    • Jenkins, J.A.1    Griffiths-Jones, S.2    Shewry, P.R.3    Breiteneder, H.4    Mills, E.N.5
  • 14
    • 5444259323 scopus 로고    scopus 로고
    • Structural, biological, and evolutionary relationships of plant food allergens sensitizing via the gastrointestinal tract
    • Mills,E.N., Jenkins,J.A., Alcocer,M.J. and Shewry,P.R. (2004) Structural, biological, and evolutionary relationships of plant food allergens sensitizing via the gastrointestinal tract. Crit. Rev. Food. Sci. Nutr., 44, 379-407.
    • (2004) Crit. Rev. Food. Sci. Nutr. , vol.44 , pp. 379-407
    • Mills, E.N.1    Jenkins, J.A.2    Alcocer, M.J.3    Shewry, P.R.4
  • 15
    • 0023737092 scopus 로고
    • Discrepancies between the skin test and IgE antibody assays: Study of histamine release, complement activation in vitro, and occurrence of allergen-specific IgG
    • van der Zee,J.S., de Groot,H., van Swieten,P., Jansen,H.M. and Aalberse,R.C. (1988) Discrepancies between the skin test and IgE antibody assays: Study of histamine release, complement activation in vitro, and occurrence of allergen-specific IgG. J. Allergy Clin. Immunol., 82, 270-281.
    • (1988) J. Allergy Clin. Immunol. , vol.82 , pp. 270-281
    • van der Zee, J.S.1    de Groot, H.2    van Swieten, P.3    Jansen, H.M.4    Aalberse, R.C.5
  • 17
    • 4344675432 scopus 로고    scopus 로고
    • In vitro assays for the diagnosis of IgE-mediated disorders
    • Hamilton,R.G. and Adkinson,N.F.Jr (2004) In vitro assays for the diagnosis of IgE-mediated disorders. J. Allergy Clin. Immunol., 114, 213-225.
    • (2004) J. Allergy Clin. Immunol. , vol.114 , pp. 213-225
    • Hamilton, R.G.1    Adkinson Jr., N.F.2
  • 19
    • 21344443033 scopus 로고    scopus 로고
    • Assessing genetically modified crops to minimize the risk of increased food allergy: A review
    • Goodman,R.E., Hefle,S.L., Taylor,S.L. and van Ree,R. (2005) Assessing genetically modified crops to minimize the risk of increased food allergy: A review. Int. Arch. Allergy Immunol., 137, 153-166.
    • (2005) Int. Arch. Allergy Immunol. , vol.137 , pp. 153-166
    • Goodman, R.E.1    Hefle, S.L.2    Taylor, S.L.3    van Ree, R.4
  • 23
    • 0037251966 scopus 로고    scopus 로고
    • SDAP: Database and computational tools for allergenic proteins
    • Ivanciuc,O., Schein,C.H. and Braun,W. (2003) SDAP: Database and computational tools for allergenic proteins. Nucleic Acids Res., 31, 359-362.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 359-362
    • Ivanciuc, O.1    Schein, C.H.2    Braun, W.3
  • 24
    • 13244265577 scopus 로고    scopus 로고
    • Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines
    • 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.
    • (2004) BMC Bioinformatics , vol.5 , pp. 133
    • Fiers, M.W.1    Kleter, G.A.2    Nijland, H.3    Peijnenburg, A.A.4    Nap, J.P.5    van Ham, R.C.6
  • 25
    • 33644504193 scopus 로고    scopus 로고
    • Development of Allergen Database for Food Safety (ADFS): An integrated database to search allergens and predict allergenicity
    • Nakamura,R., Teshima,R., Takagi,K, and 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, 32-36.
    • (2005) Kokuritsu Iyakuhin Shokuhin Eisei Kenkyusho Hokoku , pp. 32-36
    • Nakamura, R.1    Teshima, R.2    Takagi, K.3    Sawada, J.4
  • 26
    • 0031618972 scopus 로고    scopus 로고
    • The use of amino acid sequence alignments to assess potential allergenicity of proteins used in genetically modified foods
    • Gendel,S.M. (1998) The use of amino acid sequence alignments to assess potential allergenicity of proteins used in genetically modified foods. Adv. Food Nutr. Res., 42, 45-62.
    • (1998) Adv. Food Nutr. Res. , vol.42 , pp. 45-62
    • Gendel, S.M.1
  • 27
    • 0036260304 scopus 로고    scopus 로고
    • Sequence analysis for assessing potential allergenicity
    • Gendel,S.M. (2002) Sequence analysis for assessing potential allergenicity. Ann. NY Acad. Sci., 964, 87-98.
    • (2002) Ann. NY Acad. Sci. , vol.964 , pp. 87-98
    • Gendel, S.M.1
  • 28
    • 0036941115 scopus 로고    scopus 로고
    • Prediction of food protein allergenicity: A bioinformatic learning systems approach
    • Zorzet,A., Gustafsson,M. and Hammerling,U. (2002) Prediction of food protein allergenicity: A bioinformatic learning systems approach. In. Silico Biol., 2, 525-534.
    • (2002) In. Silico Biol. , vol.2 , pp. 525-534
    • Zorzet, A.1    Gustafsson, M.2    Hammerling, U.3
  • 30
    • 25444518424 scopus 로고    scopus 로고
    • 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
    • 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.
    • (2002) BMC Struct. Biol. , vol.2 , pp. 8
    • Kleter, G.A.1    Peijnenburg, A.A.2
  • 31
    • 1542316862 scopus 로고    scopus 로고
    • Statistical evaluation of local alignment features predicting allergenicity using supervised classification algorithms
    • 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.
    • (2004) Int. Arch. Allergy Immunol. , vol.133 , pp. 101-112
    • Soeria-Atmadja, D.1    Zorzet, A.2    Gustafsson, M.G.3    Hammerling, U.4
  • 32
    • 0038380463 scopus 로고    scopus 로고
    • Allergenicity prediction by protein sequence
    • Stadler,M.B. and Stadler,B.M. (2003) Allergenicity prediction by protein sequence. FASEB J., 17, 1141-1143.
    • (2003) FASEB J. , vol.17 , pp. 1141-1143
    • Stadler, M.B.1    Stadler, B.M.2
  • 33
    • 8844259689 scopus 로고    scopus 로고
    • Predicting allergenic proteins using wavelet transform
    • Li,K.B., Issac,P. and Krishnan,A. (2004) Predicting allergenic proteins using wavelet transform. Bioinformatics, 20, 2572-2578.
    • (2004) Bioinformatics , vol.20 , pp. 2572-2578
    • Li, K.B.1    Issac, P.2    Krishnan, A.3
  • 34
    • 0036772523 scopus 로고    scopus 로고
    • Data mining of sequences and 3D structures of allergenic proteins
    • Ivanciuc,O., Schein,C.H. and Braun,W. (2002) Data mining of sequences and 3D structures of allergenic proteins. Bioinformatics, 18, 1358-1364.
    • (2002) Bioinformatics , vol.18 , pp. 1358-1364
    • Ivanciuc, O.1    Schein, C.H.2    Braun, W.3
  • 35
    • 12744279638 scopus 로고    scopus 로고
    • Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins
    • 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.
    • (2005) Bioinformatics , vol.21 , pp. 39-50
    • Bjorklund, A.K.1    Soeria-Atmadja, D.2    Zorzet, A.3    Hammerling, U.4    Gustafsson, M.G.5
  • 39
    • 0033990061 scopus 로고    scopus 로고
    • Flexible sequence similarity searching with the FASTA3 program package
    • Pearson,W.R. (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol., 132, 185-219.
    • (2000) Methods Mol. Biol. , vol.132 , pp. 185-219
    • Pearson, W.R.1
  • 41
    • 0028114857 scopus 로고
    • Allergen nomenclature
    • IUIS/WHO. IUIS/WHO. Allergen Nomenclature Subcommittee
    • IUIS/WHO. (1994) Allergen nomenclature. IUIS/WHO. Allergen Nomenclature Subcommittee. Bull. World Health Organ., 72, 797-806.
    • (1994) Bull. World Health Organ. , vol.72 , pp. 797-806
  • 42
    • 0031644680 scopus 로고    scopus 로고
    • Sequence databases for assessing the potential allergenicity of proteins used in transgenic foods
    • Gendel,S.M. (1998) Sequence databases for assessing the potential allergenicity of proteins used in transgenic foods. Adv. Food Nutr. Res., 42, 63-92.
    • (1998) Adv. Food Nutr. Res. , vol.42 , pp. 63-92
    • Gendel, S.M.1
  • 44
    • 29544433190 scopus 로고    scopus 로고
    • Pollen allergens are restricted to few protein families and show distinct patterns of species distribution
    • 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.
    • (2006) J. Allergy Clin. Immunol. , vol.117 , pp. 141-147
    • Radauer, C.1    Breiteneder, H.2
  • 45
    • 0037326618 scopus 로고    scopus 로고
    • Patients with anaphylaxis to pea can have peanut allergy caused by cross-reactive IgE to vicilin (Ara h 1)
    • Wensing,M., Knulst,A.C., Piersma,S., O'Kane,F., Knol,E.F. and Koppelman,S.J. (2003) Patients with anaphylaxis to pea can have peanut allergy caused by cross-reactive IgE to vicilin (Ara h 1). J. Allergy Clin. Immunol., 111, 420-424.
    • (2003) J. Allergy Clin. Immunol. , vol.111 , pp. 420-424
    • Wensing, M.1    Knulst, A.C.2    Piersma, S.3    O'Kane, F.4    Knol, E.F.5    Koppelman, S.J.6
  • 46
    • 4043057315 scopus 로고    scopus 로고
    • Non-self-discrimination as a driving concept in the identification of an immunodominant HMW-MAA epitopic peptide sequence by autoantibodies from melanoma cancer patients
    • Dummer,R., Mittelman,A., Fanizzi,F.P., Lucchese,G., Willers,J. and Kanduc,D. (2004) Non-self-discrimination as a driving concept in the identification of an immunodominant HMW-MAA epitopic peptide sequence by autoantibodies from melanoma cancer patients. Int. J. Cancer, 111, 720-726.
    • (2004) Int. J. Cancer , vol.111 , pp. 720-726
    • Dummer, R.1    Mittelman, A.2    Fanizzi, F.P.3    Lucchese, G.4    Willers, J.5    Kanduc, D.6
  • 47
    • 33144474710 scopus 로고    scopus 로고
    • The value of short amino acid sequence matches for prediction of protein allergenicity
    • Silvanovich,A., Nemeth,M.A., Song,P., Herman,R., Tagliani,L. and Bannon,G.A. (2006) The value of short amino acid sequence matches for prediction of protein allergenicity. Toxicol. Sci., 90, 252-258.
    • (2006) Toxicol. Sci. , vol.90 , pp. 252-258
    • Silvanovich, A.1    Nemeth, M.A.2    Song, P.3    Herman, R.4    Tagliani, L.5    Bannon, G.A.6
  • 50
    • 24644440226 scopus 로고    scopus 로고
    • Assessment of sequence homology and cross-reactivity
    • Aalberse,R.C. (2005) Assessment of sequence homology and cross-reactivity. Toxicol. Appl. Pharmacol., 207, 149-151.
    • (2005) Toxicol. Appl. Pharmacol. , vol.207 , pp. 149-151
    • Aalberse, R.C.1
  • 51
    • 28644442413 scopus 로고    scopus 로고
    • External cross-validation for unbiased evaluation of protein family detectors: Application to allergens
    • Soeria-Atmadja,D., Wallman,M., Bjorklund,A.K., Isaksson,A., Hammerling,U. and Gustafsson,M.G. (2005) External cross-validation for unbiased evaluation of protein family detectors: Application to allergens. Proteins, 61, 918-925.
    • (2005) Proteins , vol.61 , pp. 918-925
    • Soeria-Atmadja, D.1    Wallman, M.2    Bjorklund, A.K.3    Isaksson, A.4    Hammerling, U.5    Gustafsson, M.G.6
  • 52
    • 8244232505 scopus 로고    scopus 로고
    • Mapping and mutational analysis of the IgE-binding epitopes on Ara h 1, a legume vicilin protein and a major allergen in peanut hypersensitivity
    • Burks,A.W., Shin,D., Cockrell,G., Stanley,J.S., Helm,R.M. and Bannon,G.A. (1997) Mapping and mutational analysis of the IgE-binding epitopes on Ara h 1, a legume vicilin protein and a major allergen in peanut hypersensitivity. Eur. J. Biochem., 245, 334-339.
    • (1997) Eur. J. Biochem. , vol.245 , pp. 334-339
    • Burks, A.W.1    Shin, D.2    Cockrell, G.3    Stanley, J.S.4    Helm, R.M.5    Bannon, G.A.6
  • 53
    • 0031767115 scopus 로고    scopus 로고
    • Naturally processed peptides from HLA-DQ7 (alpha1*0501-beta1*0301): Influence of both alpha and beta chain polymorphism in the HLA-DQ peptide binding specificity
    • Khalil-Daher,I., Boisgerault,F., Feugeas,J.P., Tieng,V., Toubert,A. and Charron,D. (1998) Naturally processed peptides from HLA-DQ7 (alpha1*0501-beta1*0301): Influence of both alpha and beta chain polymorphism in the HLA-DQ peptide binding specificity. Eur. J. Immunol., 28, 3840-3849.
    • (1998) Eur. J. Immunol. , vol.28 , pp. 3840-3849
    • Khalil-Daher, I.1    Boisgerault, F.2    Feugeas, J.P.3    Tieng, V.4    Toubert, A.5    Charron, D.6
  • 55
    • 0036740190 scopus 로고    scopus 로고
    • Recognition of core and flanking amino acids of MHC class II-bound peptides by the T cell receptor
    • Sant'Angelo,D.B., Robinson,E., Janeway,C.A. Jr and Denzin,L.K. (2002) Recognition of core and flanking amino acids of MHC class II-bound peptides by the T cell receptor. Eur. J. Immunol., 32, 2510-2520.
    • (2002) Eur. J. Immunol. , vol.32 , pp. 2510-2520
    • Sant'Angelo, D.B.1    Robinson, E.2    Janeway Jr., C.A.3    Denzin, L.K.4


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