EpiMatrix, a T-cell epitope mapping algorithm developed by the principal scientists at EpiVax, screens protein sequences for 9 to 10 amino acid long peptide segments predicted to bind to one or more MHC alleles [1,2]. EpiMatrix uses the pocket profile method for epitope prediction, which was first described by Sturniolo and Hammer in 1999. For reasons of efficiency and simplicity, predictions are limited to the eight most common HLA class II alleles and six “supertype” HLA class I alleles . EpiMatrix raw scores are normalized with respect to a score distribution derived from a very large set of randomly generated peptide sequences. Any peptide scoring above 1.64 on the EpiMatrix “Z” scale (approximately the top 5% of any given peptide set) has a significant chance of binding to the MHC molecule for which it was predicted. Peptides scoring above 2.32 on the scale (the top 1%) are extremely likely to bind; the scores of most well known T-cell epitopes fall within this range of scores.
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8 De Groot AS, Ardito M. McClaine E. Moise, L. Martinb W. Immunoinformatic comparison of T-cell epitopes contained in novel swine-origin influenza A (H1N1) virus with epitopes in 2008-09 Conventional Influenza Vaccine. Vaccine. 2009 Aug 4.Epub ahead of print.
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13. A S. De Groot. Daniel S. Rivera, J. A. McMurry, S. Buus, W. Martin, Identification of Immunogenic HLA-B7 “Achilles’ heel” Epitopes Within Highly Conserved Regions of HIV. Vaccine, 2008 26, 3059—3071.
14. De Groot, A. S. 2006. Immunomics: Discovering New Targets for Vaccine and Therapeutics. Drug Discovery Today. 11:203-209.
15 Leonard Moise, Julie A. McMurry, Soren Buus, Sharon Frey, William D. Martin and Anne S. De Groot. In Silico-Accelerated Identification of Conserved and Immunogenic Variola/Vaccinia T-Cell Epitopes, Submitted to Vaccine (David Weiner, special editor), Published Vaccine. http:/dx.doi.org/10.1016/j.vaccine.2009.06.018 Vaccine. 2009 Jun 24.
16 Gregory SH, Mott S, Phung J, Lee J, Moise L, McMurry JA, Martin W, De Groot AS.Epitope-based vaccination against pneumonic tularemia. Vaccine. 2009 Aug 27;27(39):5299-306. Epub 2009 Jul 17
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18 Sette A, Sidney J. Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics. 1999;50:201-12.
19 Sette S., Sidney J. 1999 Nine major HLA Class I supertypes account for the vast preponderance of HLA-A and –B polymorphism. Immunogenetics, 50:210-212.