Protective antigen (PA), a subunit of anthrax toxin from Bacillus anthracis, is known as a dominant com-ponent in subunit vaccines in protection against anthrax. In order to avoid the side effects of live attenuated and killed organisms, the use of linear neutralizing epitopes of PA is recommended in order to design re-combinant vaccines. The present study is aimed at determining the dominant epitopes based on multi-parameter and multi-method analysis. The epitopes were identified by the well-known online bioinformat-ics server and then they were selected and compared based on the highest score and the highest repetition rate. Further analysis on predicted epitopes has been carried out by online VaxiJen 2.0 and Protein Digest server. Among the selected epitopes, those with the highest antigenicity score (>0.9 threshold) and less susceptibility to gastrointestinal tract proteases, were selected as final epitopes. Final B-cell predicted epi-topes were amino acid residues 292-308, 507-521 and 706-719; residues 17-31, 315-329 and 385-400 which were determined as the best major histocompatibility complex I (MHCI) class of T-cells epitopes; in addition, residues 455-464 and 661-669 were also considered the best MCHII class of T-cells epitopes. Since random coil structure had a high probability of protein forming of antigenic epitope, the results of secondary structure analysis of the final PA epitopes have shown that all these epitopes form a 100% ran-dom coil structure.

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