Protein Disorder Prediction
Before starting this exercise: In the Structures tab within the Preferences dialog box (Jalview $\Rightarrow$ Preferences in Jalview desktop menu) make sure you enable the Process secondary structure from PDB and Add Temperature Factor annotation to alignment options.
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Close all windows and open the file https://www.jalview.org/tutorial/interleukin7.fa.
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Run the DisEMBL disorder predictor via the Web Service $\Rightarrow$ Protein Disorder $\Rightarrow$ Disembl with defaults.
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Select all the sequences ([CTRL]-A or [CMD]-A). Open the Structure Chooser by placing the mouse in the Sequence ID panel, right-clicking the mouse and selecting $\Rightarrow$ 3D Structure Data. . . . Select all structures in the list and then select Open new structure with button to display all the PDB structures for the sequences.
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Compare the disorder predictions to the structure data by mapping any available temperature factors to the alignment. Place the mouse in the Sequence ID panel, right-click the mouse to open the context menu and select Selection $\Rightarrow$ Add reference annotation option.
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The disorder predictors can be used to shade the sequences, select Colour $\Rightarrow$ By Annotation . . . In the dialog box tick the Per-sequence only option, select DisemblWS and Above Threshold in the drop-down menus, and select the threshold value. This shades the sequences and the structure.
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Features on sequences can conceal other colourings. This can be toggled off by selecting View $\Rightarrow$ Show Sequence Features in the alignment menu.
How well do the disordered regions predicted by each method agree with the structure?