AlphaFold 3D protein structures are now browsable from WormBase ParaSite

Only a few months after the latest release of the AlphaFold Protein Structure Database that added three-dimensional (3D) structures of complete proteomes for 7 parasitic worms, we announce the full integration of these 3D models into WormBase ParaSite.

For the first time in WormBase ParaSite, you can browse 3D protein structures visualised in a user-friendly and fun-to-explore viewer! Users can now explore the 3D protein models of their favourite genes in 8 WBPS species:

Species	Predicted structures	Links
Brugia malayi	8,743	WormBase Parasite example
Caenorhabditis elegans	19,694	WormBase ParaSite example
Dracunculus medinensis	10,834	WormBase ParaSite example
Onchocerca volvulus	12,047	WormBase ParaSite example
Schistosoma mansoni	13,865	WormBase ParaSite example
Strongyloides stercoralis	12,613	WormBase ParaSite example
Trichuris trichiura	9,564	WormBase ParaSite example
Wuchereria bancrofti	12,721	WormBase ParaSite example

Table 1. Number of structural predictions for complete proteomes of parasitic worms in AlphaFold DB v.2.1.2 and WormBase ParaSite 17.

Want to know more about how to visualise AlphaFold Protein Structure in WormBase ParaSite?

Follow this tutorial to see structural predictions for abl1 gene in Schistosoma mansoni:

1. Navigate to WormBase ParaSite and click on the Genome List button:

2. Click on your species of interest (e.g. Schistosoma mansoni) and search for abl1 gene

3. Click on the abl1 gene in the search results page:

4. We are now on the gene tab for Schistosoma mansoni abl1. This page gives us an overview of the information available at the gene level and shows the transcript table, also summary with links to external databases and a gene diagram.

5. Protein information in WormBase ParaSite is associated with transcripts of a gene. Therefore, we will navigate to the Transcript tab by clicking on the transcript ID (Smp_246700.1) in the transcript table.

6. The domains of the protein product of the transcript can be viewed graphically by clicking on Protein summary or in a table format by clicking on Domains and features. To access the 3D protein structure viewer click on AlphaFold predicted model.

7. 6/6 And more so, we can now view the shiny new interactive 3D AlphaFold structure for our protein of interest. The interactive molecular viewer visualizes the structure, coloured by the per-residue pLDDT confidence measure.

“What functionalities does the 3D protein structure viewer offer?“
The central panel (viewer) annotates the model with regions of high confidence (blue) to low confidence (orange) with its protein sequence displayed above. It’s very simple to use it: Just drag and drop with your mouse pointer to rotate the stucture and scroll to zoom in and zoom out! You can rapidly zoom in a specific residue by clicking on it in the protein sequence above the model. The right hand panel enables highlighting of one or more exons and protein features (Gene3D, PROSITE, Pfam, etc) which are controlled by clicking on the eye icon.

“More species please?“
As AlphaFold plans to expand their database in 2022 to cover additional proteomes of more species, as well as a much larger proportion of all catalogued proteins, we anticipate that more parasitic worms will make it into the AlphaFold database. WormBase ParaSite will be then able to enable “AlphaFold predicted model” viewer for these species. You can monitor the list of species present in the AlphaFold database here.

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Undoubtedly, AlphaFold opens new research horizons and we would like to encourage our users to go and explore this ground-breaking dataset in WormBase ParaSite by searching and testing the 3D protein models of your favourite worm.

We would love to hear the feedback of the helminth research community on the AlphaFold resource, the structure predictions, how you think WormBase ParaSite could facilitate your interaction with this unique dataset, or anything else. So please feel free to contact us (parasite-help@wormbase.org)