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.

Table1: Conformational parameters and positional frequencies for helix,ß-sheet and ß-turn residues.

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.

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