The Secondary Structure – Chou-Fasman track predicts secondary structure of proteins from the crystallographic structures of their amino acid sequences.

Secondary structure prediction methods from the1970s and 1980s rely on the propensities of individual amino acids observed in either alpha helices or beta strands/sheets. For a local region in the protein sequence, these propensity values are summed for each individual class. The secondary structure for central residue of the region is predicted by comparing whether propensity sum is greater than the threshold.

Chou and Fasman, 1978, identified several protein classes, with different data sets used to train the model for each class. The class for 29 Proteins, later augmented to 64 Proteins (Chou, 1990), is the more general model. The other four classes are more appropriate for specific types of protein folds: Alpha, Beta, Alpha plus Beta and Alpha/Beta (i.e., some combination of the two structural elements).

To apply this track to the sequence:

In the Tracks panel, expand Secondary Structure and check the box next to Chou-Fasman. The track will now be visible in the Analysis view

To edit track options:

Select the track in the Tracks panel. Open the Track Options section, which appears as follows:

Choose which conformation parameter table to use:

  • 29 Proteins – to use parameters from only 29 protein structures.
  • 64 Proteins – to use parameters from all 64 protein structures.
  • Alpha Class, Beta Class, Alpha plus Beta Class or Alpha/Beta Class* – to use the Chou classification method parameter tables.

If you select 29 Proteins or 64 Proteins, enter numbers in the Threshold parameters section:

  • Alpha region threshold – Pα has a default of 103.
  • Beta region threshold – Pß has a default of 105.

These values are constants which limit whether a region is defined as α-helix or ß-sheet. If Pα > 103 and Pα > Pß a region is predicted as helical. If Pß > 105 and Pß > Pα a region is predicted as a beta sheet. The default values are from Chou and Fasman (1978).

Click if you wish to return to the default value.

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