Chou–Fasman Method - 16 August 2011 - BioInformatics Pakistan

The Chou–Fasman method are an empirical technique for the prediction of secondary structures in proteins, originally developed in the 1970s.The method is based on analyses of the relative frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein structures solved with X-ray crystallography. From these frequencies a set of probability parameters were derived for the appearance of each amino acid in each secondary structure type, and these parameters are used to predict the probability that a given sequence of amino acids would form a helix, a beta strand, or a turn in a protein. The method is at most about 50–60% accurate in identifying correct secondary structures,which is significantly less accurate than the modern machine learning–based techniques.

The Chou–Fasman method takes into account only the probability that each individual amino acid will appear in a helix, strand, or turn. Unlike the more complex GOR method, it does not reflect the conditional probabilities of an amino acid to form a particular secondary structure given that its neighbors already possess that structure. This lack of cooperativity increases its computational efficiency but decreases its accuracy, since the propensities of individual amino acids are often not strong enough to render a definitive prediction.

Name P(a) P(b) P(turn) f(i) f(i+1) f(i+2) f(i+3)

Alanine 142 83 66 0.06 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

Glutamic Acid 151 037 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

The actual algorithm contains a few simple steps:

Assign all of the residues in the peptide the appropriate set of parameters.
Scan through the peptide and identify regions where 4 out of 6 contiguous residues have P(a-helix) > 100. That region is declared an alpha-helix. Extend the helix in both directions until a set of four contiguous residues that have an average P(a-helix) < 100 is reached. That is declared the end of the helix. If the segment defined by this procedure is longer than 5 residues and the average P(a-helix) > P(b-sheet) for that segment, the segment can be assigned as a helix.
Repeat this procedure to locate all of the helical regions in the sequence.
Scan through the peptide and identify a region where 3 out of 5 of the residues have a value of P(b-sheet) > 100. That region is declared as a beta-sheet. Extend the sheet in both directions until a set of four contiguous residues that have an average P(b-sheet) < 100 is reached. That is declared the end of the beta-sheet. Any segment of the region located by this procedure is assigned as a beta-sheet if the average P(b-sheet) > 105 and the average P(b-sheet) > P(a-helix) for that region.
Any region containing overlapping alpha-helical and beta-sheet assignments are taken to be helical if the average P(a-helix) > P(b-sheet) for that region. It is a beta sheet if the average P(b-sheet) > P(a-helix) for that region.
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 the f(j+1) value for the j+1 residue is used, the f(j+2) value for the j+2 residue is used and the f(j+3) value for the j+3 residue is used. If:

p(t) > 0.000075;
The average value for P(turn) > 1.00 in the tetrapeptide
The averages for the tetrapeptide obey the inequality P(a-helix) < P(turn) > P(b-sheet), then a beta-turn is predicted at that location.

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