Theoretical prediction of protein antigenic determinants from amino acid sequences

The locations of the antigenic determinants in a protein are predicted from its amino acid sequence by a modified Hopp–Woods method, proposed in this work, using both hydrophihcity and recognition factors. The amino acid – amino acid interaction energies, from which the recognition factors have been defined, have been evaluated by a semiempirical method, developed at this laboratory, using 1/R expansions parameterized on the basis of the results from accurate SCF calculations. The present procedure, which eliminates most of the uncertainties in the original Hopp–Woods method, leads to a very satisfactory prediction of the antigenic determinants.