Support vector machines for predicting HIV protease cleavage sites in protein

Knowledge of the polyprotein cleavage sites by HIV protease will refine our understanding of its specificity, and the information thus acquired is useful for designing specific and efficient HIV protease inhibitors. The pace in searching for the proper inhibitors of HIV protease will be greatly expedited if one can find an accurate, robust, and rapid method for predicting the cleavage sites in proteins by HIV protease. In this article, a Support Vector Machine is applied to predict the cleavability of oligopeptides by proteases with multiple and extended specificity subsites. We selected HIV-1 protease as the subject of the study. Two hundred ninety-nine oligopeptides were chosen for the training set, while the other 63 oligopeptides were taken as a test set. Because of its high rate of self-consistency (299/299 = 100%), a good result in the jackknife test (286/299 = 95%) and correct prediction rate (55/63 = 87%), it is expected that the Support Vector Machine method can be referred to as a useful assistant technique for finding effective inhibitors of HIV protease, which is one of the targets in designing potential drugs against AIDS. The principle of the Support Vector Machine method can also be applied to analyzing the specificity of other multisubsite enzymes. (C) 2002 John Wiley Sons, Inc.