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.

  1. Close all windows and open the file

  2. Run the DisEMBL disorder predictor via the Web Service $\Rightarrow$ Protein Disorder $\Rightarrow$ Disembl with defaults.

  3. 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.

  4. 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.

  5. 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.

  6. 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?

For more information on this topic go to section 8.2 of the Jalview manual.
 This exercise can be viewed in the Protein disorder predictors video.