The Chou-Fasman algorithm for the prediction of protein secondary structure is one of the most widely used predictive schemes.The Chou-Fasman method of secondary structure prediction depends on assigning a set of prediction values to a residue and then applying a simple algorithm to the conformational parameters and positional frequencies. The Chou-Fasman algorithm is simple in principle.The conformational parameters for each amino acid were calculated by considering the relative frequency of a given amino acid within a protein, its occurrence in a given type of secondary structure, and the fraction of residues occurring in that type of structure. These parameters are measures of a given amino acid's preference to be found in helix, sheet or coil. Using these conformational parameters, one finds nucleation sites within the sequence and extends them until a stretch of amino acids is encountered that is not disposed to occur in that type of structure or until a stretch is encountered that has a greater disposition for another type of structure. At that point, the structure is terminated. This process is repeated througout the sequence until the entire sequence is predicted.

The actual algorithm for turn prediction consists of following steps:

To identify a bend at residue number j, calculate the following value:

p(t)=f(j)*f(j+1)*f(j+2)*f(j+3)

where f(j), f(j+1), f(j+2) and f(j+3) are bend frequencies in the four positions on the beta turn.

If:

p(t)>0.000075;

the average value for P(turn)>1.00 in the tetrapeptide where P(turn) is the conformational parameter for ß-turn ; and
the averages for the tetrapeptide obey the inequality P(helix)<P(turn)>P(sheet), then a ß-turn is predicted at that location where P(helix) and P(sheet) are the conformational parameters for helix and sheet respectively.

 Name P(a) P(b) P(turn) f(i) f(i+1) f(i+2) f(i+3) Alanine 142 83 66 0.060 0.076 0.035 0.058 Arginine 98 93 95 0.070 0.106 0.099 0.085 Aspartic acid 101 54 146 0.147 0.110 0.179 0.081 Asparagine 67 89 156 0.161 0.083 0.191 0.091 Cysteine 70 119 119 0.149 0.050 0.117 0.128 Glumatic acid 151 37 74 0.056 0.060 0.077 0.064 Glutamine 111 110 98 0.074 0.098 0.037 0.098 Glycine 57 75 156 0.102 0.085 0.190 0.152 Histidine 100 87 95 0.140 0.047 0.093 0.054 Isoleucine 108 160 47 0.043 0.034 0.013 0.056 Leucine 121 130 59 0.061 0.025 0.036 0.070 Lysine 114 74 101 0.055 0.115 0.072 0.095 Methionine 145 105 60 0.068 0.082 0.014 0.055 Phenylalanine 113 138 60 0.059 0.041 0.065 0.065 Proline 57 55 152 0.102 0.301 0.034 0.068 Serine 77 75 143 0.120 0.139 0.125 0.106 Threonine 83 119 96 0.086 0.108 0.065 0.079 Tryptophan 108 137 96 0.077 0.013 0.064 0.167 Tyrosine 69 147 114 0.082 0.065 0.114 0.125 Valine 106 170 50 0.062 0.048 0.028 0.053

P(a), P(b) and P(turn) are conformational parameters of helix,ß-sheet and ß-turns.