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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Improved Chou-Fasman method for protein secondary structure prediction

This is an open access article distributed under the terms of the Creative Commons Attribution License http: Assessment of secondary-structure prediction of proteins comparison of computerized Chou-Fasman method with others.

It indicates that many coil positions are incorrectly predicted as helices or strands in CFM that causes high false positive in CFM.

Dominant forces in protein folding. 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.

According to the analysis above, a was set as 9. Besides statistic methods, there are several sequence analysis approaches proposed for protein secondary structure prediction based on the physicochemical property of residues.

We compared the indices with those obtained from the original Chou-Fasman method and other four popular methods. However, by use of sequence alignment, the class of protein with unknown structure may be decided.


It is able to predict protein secondary structure as good as current popular methods. Hence, the coefficients of CWT can be calculated by the difference of convolution of s [k] and the integral formula. It may be a possible way to solve this problem by using Cgou to look for the scale of cho, strand, and coil, respectively.

The data set CB please see Supplementary file “dataset. When helix or strand is buried inside of a protein, their residues are more hydrophobic. First, the hydrophobicity value based CWT technology was used to calculate the number and locations of protein secondary structure segments, and then substituted the nucleation regions of Algorighm with these positions. Predicting one-dimensional protein structure by profile-based neural networks.

Three commonly used indices were adopted to assess our method. We classified this data set into four classes based on the protein structural classification database SCOP [ 35 ].

CFSSP: Chou & Fasman Secondary Structure Prediction Server

A novel approach to predicting protein structural classes in a -D amino acid composition space. Vhou Opin Struct Biol. Select a prediction algoritum or choose the methods to be compared Chou-Fasman GOR Neural Network Input the amino acid sequence by one of the following ways Upload the amino acid sequence file flat format: It is also fast and low computational consumption although the CWT method had been brought in our method because it doesn’t need to do training and sequence alignment.

Protein secondary structure prediction with a neural network.


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. From this result, it can be found that each modification has improved several indices while other indices are nearly invariant. Results We improved Chou-Fasman method in three aspects. Fasman Chapter 9: We tested sequential 5 numbers beside the average number with the interval of 0.

Sejnowski Predicting fwsman secondary structure of globular proteins using neural network models. That means the light bands are more hydrophobic than the dark ones.

Chou-Fasman Parameters

This transcendental condition has narrowed the application area of our method. To improve the second rule, folding type-specific structure propensities were used instead of traditional Chou-Fasman parameters to extend the secondary structure segments and to deal with the overlapped regions. Table 6 The degree of improvement with 3 different steps of our method.

Discussion By use of cross validation, all the results calculated in this article are reliable. To deal with these problems, further modifications are needed to improve our method: The referenced secondary structure for each position was defined by DSSP [ 32 ]. In addition, coil propensities can be included in protein secondary structure prediction for reducing over prediction.