AIDSWEEKLY Plus, Monday, 18 November 1996
Daniel J. DeNoon, Senior Editor

The product, EpiMatrix/HIV, was developed at Brown University and implemented for the Internet by AVX Design Inc., Providence, Rhode Island. Both a website and an online tool, EpiMatrix is located on the Internet at http://www.epimatrix.com/hiv.

EpiMatrix is a computer-driven algorithm. Given a number of primary HIV protein sequences, it predicts the sequences most likely to bind to major histocompatibility complex (MHC) molecules.

"Selection of peptides that are highly likely to bind to MHC will enable the identification of both T-helper and cytotoxic T-cell (CTL) epitopes, which are critical components of HIV vaccines," noted Anne S. De Groot of Brown University and Greg Deocampo of AVX. "Utilization of this computer algorithm by HIV vaccine researchers may reduce the cost and labor associated with HIV vaccine research by two to twenty fold."

The site is linked to the Los Alamos database of HIV sequences and can thus access all HIV sequences in the public domain. These sequences include more than 400 separate HIV-1 proteins from all of the viral clades.

"The web format will enable updates and exchange of information among users," De Groot and Deocampo suggested. "This online tool should advance the development of globally relevant and accessible HIV vaccines."

The EpiMatrix algorithm yields a score for each peptide. The peptides are scored in a 10-mer frame. Scoring is a quantitative estimate of the likelihood (relative to other sequences) that a peptide will bind to a given human leukocyte antigen (HLA) molecule.

There are two scoring methods: single-allele predictions score for specific HLA alleles and clustered predictions score peptides by the prevalence of MHC alleles in selected populations.

"Matrices for all of the major (greater than 10 percent population prevalence) MHC alleles representing world populations will be included in the algorithm," wrote Brown researcher Bill M. Jesdale and colleagues in the preprint of an article to be published in Vaccines '97, Cold Spring Harbor Laboratory Press.

"EpiMatrix will reduce the total number of regions of HIV proteins to be evaluated in in vitro assays, permitting more rapid resolution of pressing research questions related to HIV vaccine development and research on HIV immunopathogenesis."

EpiMatrix/HIV is available at no charge thanks to funding from the National Institute of Allergy and Infectious Diseases Division of AIDS.

The site became available on November 1, 1996.

In earlier work, De Groot and colleagues referred to the algorithm as EpiMer (see AIDS Weekly Plus, May 27, 1996; and Roberts et al., AIDS Research and Human Retroviruses, May 1, 1996;12(7):593-610).

The corresponding authors of the EpiMatrix announcement are Anne S. De Groot, TB/HIV Research Laboratory, International Health Institute, Brown University School of Medicine, Box G/B 473, Providence, Rhode Island 02912; Email: anne_degroot@brown.edu; and Greg Deocampo, AVX Design Inc., 184 Kinsley Avenue, Providence, Rhode Island 02903; Email gregdeocampo@avx.com.

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