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.

1 De Groot, AS, Jesdale, BM, Szu, E, Schafer, JR. An interactive web site providing MHC ligand predictions: application to HIV research. AIDS Res. and Human Retroviruses. 1997;13: 539-541.

2 Schafer JA, Jesdale BM, George JA, Kouttab NM, De Groot, AS. Prediction of well-conserved HIV-1 ligands using a Matrix-based Algorithm, EpiMatrix. Vaccine. 1998;16(19):1880-1884.

3 Sette A, Sidney J. HLA supertypes and supermotifs: a functional perspective on HLA polymorphism, Current Opinions in Immunology. 1998;10:478-482.

4 Panina-Bordignon P, Tan A, Termijtelen A, Demotz S, Corradin G, Lanzavecchia A. Universally immunogenic T cell epitopes: promiscuous recognition by T cells, European Journal of Immunology 1989 19:2237-2242.

5 De Groot AS, Clerici M, Hosmalin A, Hughes SH, Barnd D, Hendrix CW, Houghten R, Shearer GM, Berzofsky JA. Human Immunodeficiency virus reverse transcriptase T helper epitopes identified in mice and humans: correlation with a cytotoxic T cell epitope, J. Infect Dis, 1991 164:1058-1065.

6 De Groot AS, Rivera DS, McMurry JA, Buus S, Martin W, Identification of Immunogenic HLA-B7 “Achilles’ heel” Epitopes Within Highly Conserved Regions of HIV. Vaccine, 2008;26:3059-3071.

7 De Groot AS, Marcon L, Bishop EA, Rivera D, Kutzler M, Weiner DB, Martin W. HIV vaccine development by computer assisted design: the GAIA vaccine. Vaccine. 2005 Mar 18; 23 [7-18):2136-48.

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.

9 Lichterfeld M, Williams KL, Mui SK, Shah SS, Mothe BR, Sette A, Kim A, Johnston MN, Burgett N, Frahm N, Cohen D, Brander C, Rosenberg ES, Walker BD, Altfeld M, Yu XG T cell receptor cross-recognition of an HIV-1 CD8+ T cell epitope presented by closely related alleles from the HLA-A3 superfamily. Int Immunol. 2006 Jul;18(7):1179-88.

10 Frahm N, Korber BT, Adams CM, Szinger JJ, Draenert R, Addo MM, Feeney ME, Yusim K, Sango K, Brown NV, SenGupta D, Piechocka-Trocha A, Simonis T, Marincola FM, Wurcel AG, Stone DR, Russell CJ, Adolf P, Cohen D, Roach T, StJohn A, Khatri A, Davis K, Mullins J, Goulder PJ, Walker BD, Brander C. Consistent cytotoxic-T-lymphocyte targeting of immunodominant regions in human immunodeficiency virus across multiple ethnicities. J Virol. 2004;78:2187-200.

11. Page KR, Scott AL, Manabe YC. The expanding realm of heterologous immunity: friend or foe? Cell Microbiol. 2006 Feb;8(2):185-96.

12. De Groot AS, Bishop EA, Khan B, Lally M, Marcon L, Franco J, Mayer KH, Carpenter CC, Martin W. Engineering immunogenic consensus T helper epitopes for a cross-clade HIV vaccine. Methods. 2004 Dec; 34(4):476-87 Bioinformatics in Vaccine Design.

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

17 De Groot AS, Berzofsky JA. From genome to vaccine—new immunoinformatics tools for vaccine design. Methods 2004;34: 425–8.

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.


  • April 15, 2016

    ISV & Vaccine Renaissance Conference – CALL FOR ABSTRACTS!

    The 2016 ISV Annual Congress in collaboration with Vaccine Renaissance X and DNA Vaccine will be held in Boston, Massachusetts, United States on Oct. 2-4, 2016.    Registration abstract is opening soon! The planning committee encourages you to submit an abstract for consideration! Abstract Submission Deadline: June 24th Abstract Decision Deadline: July 15th   http://www.isvcongress.org/
  • March 11, 2016

    10th Annual Vaccine Renaissance Save the Date Postcard

    CLICK HERE to see the save the date postcard for 2016 ISV Conference
  • February 19, 2016

    iCubed Team Members Making Moves

    This past week at iCubed, Dr. Barbara Lohman Payne received a new title of Associate Research Professor. Barbara joined iCubed and URI as a Research Assistant Professor in 2013, with the Laboratory of Viral Immunity and Pathogenesis. Dr. Lohman-Payne’s area of research is viral immunopathology, with special interest in the impact of HIV exposure in ...