Bioinformatics for characterisation of allergens, allergenicity and allergic crossreactivity.

Allergies are a major cause of chronic ill health in industrialised countries with the incidence of reported cases steadily increasing. This Research Focus details how bioinformatics is transforming the field of allergy through providing databases for management of allergen data, algorithms for characterisation of allergic crossreactivity, structural motifs and B- and T-cell epitopes, tools for prediction of allergenicity and techniques for genomic and proteomic analysis of allergens.

[1]  Simon Kasif,et al.  Computational methods in molecular biology , 1998 .

[2]  A. Sidoli,et al.  Cutting edge: identification of novel T cell epitopes in Lol p5a by computational prediction. , 1999, Journal of immunology.

[3]  Kenji Matsumoto,et al.  Human Mast Cell Transcriptome Project , 2001, International Archives of Allergy and Immunology.

[4]  Jaap Heringa,et al.  Local Weighting Schemes for Protein Multiple Sequence Alignment , 2002, Comput. Chem..

[5]  C. Blanco.  Latex-fruit syndrome , 2003, Current allergy and asthma reports.

[6]  Kun Yu,et al.  Methods for Prediction of Peptide Binding to MHC Molecules: A Comparative Study , 2002, Molecular medicine.

[7]  P. Bhalla,et al.  Hypoallergenic derivatives of major grass pollen allergens for allergy vaccination , 2003, Immunology and cell biology.

[8]  Santa Jeremy Ono,et al.  Molecular genetics of allergic diseases. , 2000, Annual review of immunology.

[9]  R W R Crevel,et al.  Assessment of the potential allergenicity of ice structuring protein type III HPLC 12 using the FAO/WHO 2001 decision tree for novel foods. , 2003, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[10]  A. Silvanovich,et al.  Bioinformatic Methods for Allergenicity Assessment Using a Comprehensive Allergen Database , 2002, International Archives of Allergy and Immunology.

[11]  U. Şahin,et al.  Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices , 1999, Nature Biotechnology.

[12]  S Vieths,et al.  Cross-reactivity and epitope analysis of Pru a 1, the major cherry allergen. , 1999, Molecular immunology.

[13]  M. W. Mueller,et al.  Microarrayed recombinant allergens for diagnosis of allergy , 2003, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[14]  Werner Braun,et al.  SDAP: database and computational tools for allergenic proteins , 2003, Nucleic Acids Res..

[15]  R. Aalberse,et al.  Structural biology of allergens. , 2000, The Journal of allergy and clinical immunology.

[16]  Zukang Feng,et al.  The Protein Data Bank and structural genomics , 2003, Nucleic Acids Res..

[17]  Kenneth H. Fasman,et al.  Chapter 3 - An introduction to biological sequence analysis , 1998 .

[18]  T Sasazuki,et al.  Magnitude of structural changes of the T-cell receptor binding regions determine the strength of T-cell antagonism: molecular dynamics simulations of HLA-DR4 (DRB1*0405) complexed with analogue peptide. , 2000, Protein engineering.

[19]  F. Montealegre,et al.  Cloning and expression of Blo t 1, a novel allergen from the dust mite Blomia tropicalis, homologous to cysteine proteases , 2003, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[20]  Kevin Karplus,et al.  A Flexible Motif Search Technique Based on Generalized Profiles , 1996, Comput. Chem..

[21]  Vladimir Brusic,et al.  Prediction of promiscuous peptides that bind HLA class I molecules , 2002, Immunology and cell biology.

[22]  B. Chiang,et al.  Proteomics and Immunological Analysis of a Novel Shrimp Allergen, Pen m 21 , 2003, The Journal of Immunology.

[23]  D. Flower,et al.  Quantitative approaches to computational vaccinology , 2002, Immunology and cell biology.

[24]  R. Valenta,et al.  Recombinant allergen molecules: tools to study effector cell activation , 2001, Immunological reviews.

[25]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[26]  W R Pearson,et al.  Flexible sequence similarity searching with the FASTA3 program package. , 2000, Methods in molecular biology.

[27]  F. Shakib,et al.  The molecular basis of allergenicity: comparative analysis of the three dimensional structures of diverse allergens reveals a common structural motif , 2001, Molecular pathology : MP.

[28]  R. Crevel,et al.  Sequence analysis and resistance to pepsin hydrolysis as part of an assessment of the potential allergenicity of ice structuring protein type III HPLC 12. , 2002, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[29]  Yssel,et al.  Identification of a highly promiscuous and an HLA allele‐specific T‐cell epitope in the birch major allergen Bet v 1: HLA restriction, epitope mapping and TCR sequence comparisons , 1999, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[30]  M. Degano,et al.  Crystal structure of a hypoallergenic isoform of the major birch pollen allergen Bet v 1 and its likely biological function as a plant steroid carrier. , 2003, Journal of molecular biology.

[31]  J. Thompson,et al.  Multiple sequence alignment with Clustal X. , 1998, Trends in biochemical sciences.

[32]  S. Gendel,et al.  Sequence Analysis for Assessing Potential Allergenicity , 2002, Annals of the New York Academy of Sciences.