Thornton's frequencies

In 1988, Janet Thornton developed a prediction program based on the statistical method employed by Chou and Fasman (1977). Initially, the absolute amino acid occurrences for each of the 4 positions in the ß-turn type categories were calculated. These were then normalized to give positional frequencies f(i), f(i+1), f(i+2), f(i+3), which were used by the predictive algorithm. Conformational parameters for the turn categories, P(t), were also calculated for each amino acid. The conformational parameters for helix, P(a) and ß-sheet, P(b) were taken from Chou & Fasman (1978).

The parameters used by the program were defined as follows:

p(Aa)=f(Aa)/<f>

where:

f(Aa)=no.of particular amino acid type of secondary structure/no.of particular amino acid in proteins studied

<f>=total no. of amino acids in type of secondary structure/total no. of amino acids in proteins studied

for positions i to i+3:

f(iAa)=no.of particular amino acid in position i of turn/no.of particular amino acid in proteins studied

The algorithm used the following criteria to test for a particular ß-turn type:

1. p(t)=f(i)*f(i+1)*f(i+2)*f(i+3) was greater than a calculated cutoff value.

cutoff value for Type-I ß-turn=4.00

cutoff value for Type-II ß-turn=2.70

2. <P(t)> was greater than unity.

3. <P(t)> was greater than either <P(a)> or <P(b)>.

The cutoff values were obtained by the "fine tuning" of the average probability of occurrence of that particular ß-turn type. The average probability is the average of the p(t) values for every possible 4 residue sequence. The fine tuning was in the form of a multiplication factor, which , when applied to the average probability, maximized the number of database-located turns of a particular type found by criterion 1, and minimized the number of 4-residue sequences in the proteins studied that were not turns, but satisfied criteria 2 and 3.

Table2: Conformational parameters and positional frequencies

A. Type I ß-turns

B. Type-II ß-turns

Using the appropirate average probability of ß-turn occurence as a starting probability of ß-turn occurence as a starting point, the cut-off was adjusted to maximize the number of observed turns predicted and minimize the number of incorrectly predicted turns (Thornton 1988).

Back to submission form