PRECISE PREDICTION OF MAJOR HISTOCOMPATIBILITY COMPLEX CLASS-II PEPTIDE INTERACTION BASED ON PEPTIDE SIDE-CHAIN SCANNING

We describe here a new method for predicting class II major histocompa tibility complex-binding peptides, based on the preferences observed i n a systematic series of peptide binding experiments where each positi on in a ''minimal'' peptide was replaced individually by every amino a cid. The DRB1()0401 peptide binding preferences were determined and i ncorporated into a computer program that looks through sequences for p otential epitopes and assigns each a score. These scores correlate wel l with previously determined T cell epitopes of foreign antigens and e ndogenous peptides from self proteins. Our findings hold implications for the design of subunit vaccines and in the identification of autoan tigenic peptide regions within self proteins.