A COMPUTER-PROGRAM FOR PREDICTING POSSIBLE CYTOTOXIC T-LYMPHOCYTE EPITOPES BASED ON HLA CLASS-I PEPTIDE-BINDING MOTIFS

Vaccination with peptides recognized by antigen-specific CTLs can prev ent lethal virus infections and tumor growth. In order to avoid the sy nthesis and testing of the numerous overlapping peptides of long AA se quences of proteins of interest, we developed a computer program which utilizes the rules, ''motifs'' which govern how peptides bind to HLA class I molecules, to derive a predicted binding score for each overla pping peptide. Correlations between the predicted and actual binding r esults to HLA-A()0201 for 100 peptides selected from six early and tw o late protein sequences of human papilloma-virus type 1a revealed an acceptable level (61%) of concordance. The program is very flexible wi th regard to the input of protein sequences and motif definitions and is able to handle various motif and peptide lengths.