Application of a modified computer algorithm in determining potential antigenic determinants associated with the AIDS virus glycoprotein

A computer program was developed for use on an Apple IIe that utilized the parameters developed by Hopp and Woods ( T. P. Hopp and K. R. Woods, 1983, Mol. Immunol. 20, 483–489) for predicting the hydrophilic regions of a given protein. This program will produce a listing of the hydrophilic sequence averages and graphically illustrates the peak areas. The hydrophilic averages over a hexapeptide length can be used to predict protein structure. In conjunction with the Chou-Fasman predictive scheme for protein secondary structure determination, the possible antigenic determinants for the envelope glycoprotein of three viruses isolated from patients with acquired immunodeficiency syndrome (AIDS) were predicted. These predicted determinants could be used to generate synthetic peptides that represent a potential vaccine preparation or in developing a diagnostic assay that specifically detects the agent.