HIV-2 proteaseAgain, for facilitating comparison, the training set used in the h function method (Poorman et al。, 1991) for HTV-2 protease was used here。
The set consists of 22 oligopeptides, with 21 octapeptides and one heptapeptide。 The values of Pi(X) (i = 1,2, 。 。 。,8) obtained through this training set are listed in Table VI。
Based on these values, 10 000 octapeptides were generated by Monte Carlo sampling and they formed an expanded training set for HTV-2 protease。
Based on the expanded training set, the 800 conditional probability values were derived。 For the same reason as stated above for HTV-1 protease, before substituting these data into equations (3), (6) or (8) to calculate n , the following procedure was taken。
If a non-conditional probability equals zero, e。g。 Pi(A) = 0 (i = 1,2, 。 。 。,8), then it should be replaced by。If a conditional probability equals zero, e。
g。 Pj(A│C) = 0 (j = 4 or 6), then it should be replaced by。The 10 000 octapeptides thus generated by Monte Carlo sampling and the 800 conditional probability values derived from HTV-2 protease are stored in the computer and they are also available upon request。
With these data, one can calculate n from equation (3), (6) or (8) for any given octapeptide or heptapeptide。 Again, the amplifying factor f = 10" was taken in calculating II for HTV-2 protease。
It remains to determine the value of threshold e for HTV-2 protease for which we used the same optimization procedure as described above for the HTV-1 protease。
The 22 cleavable oligopeptides were taken from Table VII and the non-cleavable peptides were taken again from the sequence of hen egg lysozyme。
Indeed, in this protein, no HTV-2 protease cleavage sites were detected even after complete denaturation (J。Hui, unpublished results)。
The optimization process is illustrated through Table VIE, where we can see that the total number of correct predictions reaches a maximum value of 144 when e = 1。
8, which was taken as the threshold for HIV-2 protease。 Using this value, we can calculate A via equation (5)。 The predicted results for the 22 oligopeptides in the HTV-2 protease training set are listed in Table VQ。
The values of A are all > 0, meaning that all these oligopeptides can be cleaved by HTV-2 protease, implying that the 2 - 4 - 6 subsite-coupled model is fully selfconsistent within the cleavable training set。
Also it can be seen from Table VQ that incorrect predictions were obtained for two of the 22 oligopeptides if the h function method was applied。
For the 122 octapeptides taken from the sequence of hen egg lysozyme, they all were found to have negative values of A, meaning the current method is also fully self-consistent with the non-cleavable training set。
The 52 oligopeptides, investigated recently by means of kinetic analysis (T6zser et al。, 1992), are listed in Table DC。
This is an independent set of oligopeptides that is outside of the development set in Table VII and it can be used to test the extrapo。