CFSSP is a online program which predicts secondary structure of the protein. In this program Chou & Fasman algorithm is implemented. This exercise teaches how to use the Chou-Fasman Interactive. The Chou- Fasman method predicts protein secondary structures in a given protein sequence. Predict locations of alpha-helix and beta-strand from amino acid sequence using Chou-Fasman method, Garnier-Osguthorpe-Robson method, and Neural.
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The A,gorithm method is an empirical technique for the prediction of secondary structures in proteinsoriginally developed in the s by Peter Y. Chou and Gerald D. From these frequencies a set of probability parameters were derived for the appearance of each amino fasnan 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 original Chou—Fasman parameters found some strong tendencies among individual amino acids to prefer one type of secondary structure over others. Alanineglutamateleucineand methionine were identified as helix formers, while proline and glycinedue to the unique conformational properties of their peptide bondscommonly end a helix. The original Chou—Fasman parameters  were derived from a very fasmaan and non-representative sample of protein structures due to the small number of such structures that were algorirhm at the time of their original work.
Improved Chou-Fasman method for protein secondary structure prediction
These original parameters have since been shown to be unreliable  and have been updated from a current dataset, along with modifications to the initial algorithm. The Chou—Fasman method takes into account only the algogithm that each individual amino acid will appear in a helix, strand, or turn.
Unlike the more complex GOR methodit 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. The Chou—Fasman method predicts helices and strands in a similar fashion, first searching linearly through the sequence for a “nucleation” region of high helix or strand probability and then extending the region until a subsequent four-residue window carries a probability of less than 1.
As originally described, four out of any six contiguous amino acids were sufficient to nucleate helix, and three out of any contiguous five were sufficient for a sheet. The probability thresholds for helix and strand nucleations are constant but not necessarily equal; originally 1.
Turns are also evaluated in four-residue windows, but are calculated using a multi-step procedure because many turn regions contain amino acids that could also appear in helix or xlgorithm regions. Four-residue cohu also have their own characteristic amino acids; proline and glycine are both common in turns.
A turn is predicted only if the turn probability is greater than the helix or sheet probabilities and a probability value based on the positions of particular amino acids in the turn exceeds a predetermined threshold.
CFSSP: Chou & Fasman Secondary Structure Prediction Server
The turn probability p t is determined as:. If p t exceeds an arbitrary cutoff value originally 7.
If the first two conditions are met but the probability of a beta sheet p b exceeds p tthen a sheet is predicted instead. From Wikipedia, the free encyclopedia. Prediction of the secondary structure of proteins from their amino acid sequence.