Tutorial: Display variants on AlphaFold-predicted 3D protein structures

You’ve sequenced your samples and identified variants. Great!

Now, here’s how you can use WormBase ParaSite’s new feature to find out the effect of your variants on 3D AlphaFold protein structures and interactions:

  1. The Variant Effect Predictor (VEP) is what you’re going to need for this task. You can find it in the Tools page of WormBase ParaSite.

2. Click the ‘Variant Effect Predictor’ button to open the VEP web tool and enter your input data using instructions in the documentation:

3. Now, make sure that the ‘Protein domains’ option from the ‘Protein Annotation’ panel is selected. It will retrieve overlapping protein domains from

When the “Protein domains” option is selected, as well as reporting the IDs of overlapping protein domains, the VEP output will also show links to a 3D protein viewer if a missense variant overlaps an Alphafold 3D protein model.

4. Now click the ‘Run’ button to submit the VEP query… et voilá!

5. Click on the ’AlphaFold Model’ button in the ‘Protein Matches’ column to launch the interactive AlphaFold protein structure visualisation.

. 8/ You can now browse the 3D protein structure. Exons/protein domains can be displayed to provide more context. Use your mouse to rotate and zoom in/out the model. Click on the ‘Focus’ button to zoom in to the variant of interest.


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