[Amino acid similarity matrix for detecting the antigenically similar sequences in non-related proteins]

A special matrix of amino acid antigenic similarity for computer detection of the potential antigenic proximity of unrelated proteins is proposed. The matrix was built using the data concerning affinities of amino acid residue interactions between subunits in oligomeric proteins. The diagonal elements of the matrix characterize the recognition of amino acid residues and the non-diagonal ones represent the relative similarity measure of antibody--amino acid residue interactions specificity. The application of the new matrix for comparing proteins allows the hydrophilic potentially immunologically active regions of sequences to be picked out as similar fragments. When the influenza virus hemagglutinin was compared with 116 human proteins, eight fragments were picked out, that could not be determined by means of the routinely used MDM78 matrix. The antigenic similarity matrix for defining the forbidden structures is proposed to be used for preparing the peptidic antiviral vaccines.