How to overlay likely pathogenic variants from Platform/Portal in alphafold predicted structure

Data Access
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Systematically overlaying likely pathogenic variants over @DeepMind #alphafold predicted structures provides a unique opportunity to dive into the mechanisms of disease.

Here, I describe how to get the Platform variants (from genetics portal and ClinVar - EVA) overlaid in the 3D structure. I’ll focused on NOD2 a protein known to be involved in several inflammatory diseases.

Full video - NOD2 and disease variation - YouTube

First you need to get the variation data from the Platform evidence dataset:

Next you need to overlay this information in the 3d model provided by AlphaFold. Here an example using Pymol:

The rest is some amazing video skills from @hcornu!