Secondary Structure Prediction for Aligned Amino Acid Sequences (ver. 0.9)

Predict locations of alpha-helix and beta-strand for the amino acid sequences processed through Alignment.

1. Select a prediction method or choose the methods to be compared
   
   Chou-Fasman GOR Neural Network
   
   
2. Input the amino acid sequences as a result of alignment by one of the following ways
   (Alignment can be built here from FASTA sequences)
   
   
   1. Upload the file (txt file):
   2. Paste the aligned amino acid sequences in the box:
   
   
   

The method is implemented in this server based on the descrption in the following paper;
Peter Prevelige, Jr. and Gerald D. Fasman (1989) Chapter 9: Chou-Fasman Prediction of the Secondary Structure of Proteins: The Chou-Fasman-Prevelige Algorithm. in Prediction of Protein Structure and the Principles of Protein Conformation (edited by Gerald D. Fasman), Plenum, New York, pp.391-416 (ISBN 0306431319).
Garnier, J., Osguthorpe, D.J., and Robson, B. (1978) Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120, 97-120.
Ning Qian and Terrence J. Sejnowski (1988) Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol. 202, 865-884.

The Principle in Chou and Fasman method

Secondary structure prediction method by Chou and Fasman (CF) is one of the oldest and simplest method. The method was originally presented in 1974 and later improved in 1977, 1978, 1979, 1985 and 1989.

CF depends on observed frequency of types of amino acid residues in alpha-elix, beta strand, beta turn, and other structures in protein three-dimensional structures. ....

The Principle in GOR method

Secondary structure prediction method by GOR is one of the popular method utilizing information theory.

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The Principle in Neural Network method

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