The Secondary Structure Prediction plugin provides a set of algorithms for the protein secondary structure (alpha-helix, beta-sheet) prediction from a raw sequence.

Currently available algorithms are:

You can access these analysis capabilities for a protein sequence using the Analyze ‣ Predict secondary structure... context menu item. The dialog will appear:

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     <img src="/wiki/download/attachments/4227669/Secondary Structure Prediction.png"/>
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It supports the following options:

Algorithm — you can choose the preferred algorithm. Currently, “GORIV” and “PsiPred” algorithms are available.

Range start / Range end — select the sequence range for prediction.

Results — visual representation of the prediction results, for example:

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     <img src="/wiki/download/attachments/4227669/Secondary Structure Prediction_1.png"/>
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Save as annotation — select this button to save the results as annotations of the current protein sequence.