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:

SpeciesPredicted structuresLinks
Brugia malayi8,743WormBase Parasite example
Caenorhabditis elegans19,694WormBase ParaSite example
Dracunculus medinensis10,834WormBase ParaSite example
Onchocerca volvulus12,047WormBase ParaSite example
Schistosoma mansoni13,865WormBase ParaSite example
Strongyloides stercoralis12,613WormBase ParaSite example
Trichuris trichiura9,564WormBase ParaSite example
Wuchereria bancrofti12,721WormBase 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:
  1. Click on your species of interest (e.g. Schistosoma mansoni) and search for abl1 gene

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

  1. 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.

  1. 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.
  1. 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.
  1. 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.


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)

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Announcing WormBase ParaSite release 17

Have you been waiting for our next release? The wait is finally over! Despite being understaffed and underfunded, WormBase ParaSite launches its new release 17 with an exciting list of new/updated genomes and new features:

  • Integration of AlphaFold 3D protein structures for 8 species.
  • Addition of 11 new genome assemblies of which 6 are new species.
  • Annotation updates for 2 genomes.
  • Gene-phenotype associations are now available in our FTP directory.
  • Improvements in the way external gene synonyms are integrated and displayed.
  • Deployment of WebApollo instances for more species to further facilitate community curation.

New Species

Angiostrongylus vasorum – a clinically important parasitic nematode living in the arteries and heart of several canid species, including domestic dogs (from Tayrov et al., 2021).
Cercopithifilaria johnstoni – a filarial nematode transmitted by hard ticks to infect a broad native Australian murid and marsupial hosts (from McCann et al., 2021).
Fasciolopsis buski – a large fluke that infects the small intestine of humans and pigs in East/Southeast Asia (from Choi et al., 2020).
Gyrodactylus bullatarudis –  monogenean parasite of the guppy fish (from Konczal et. al, 2020).
Halicephalobus spNKZ332 – small, parthenogenic clade IV nematode isolated from termites in Japan (from Ragsdale et al., 2019).
Heterodera schachtii – a.k.a the beet cyst nematode, is a plant pathogenic parasite which can infect more than 200 plants including the model plant Arabidopsis thaliana (from Siddique et al., 2021).


Assembly Updates

Schistosoma mansoni
We are proud to present the best ever S. mansoni assembly created until the next one! S. mansoni (blood fluke) is one of the three major infectious agents responsible for the chronic debilitating disease schistosomiasis found throughout Africa and South America. Its previous assembly (v7) was substantially upgraded following the incorporation of HiC data, and further PacBio analysis to resolve repeats leading to the new, near-complete chromosomal assembly (v9) presented in this release! More information can be found in this pre-print by Buddenborg et al 2021.

Fasciola hepatica
This sheep liver fluke or common liver fluke, is a parasite that infects humans, cows and sheep, causing fascioliasis. The previous assembly and annotation which were submitted in 2013 were drastically improved in this release as described by McNulty et al., 2017.

Heterodera glycines
The soybean cyst nematode (SCN), Heterodera glycines, is a plant-parasitic nematode infecting soybean roots. The previous assembly and annotation which were submitted in 2013 were drastically improved in this release as described by Masonbrink et al., 2021.


Annotation updates


AlphaFold 3D protein structures are now browsable from 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:

SpeciesPredicted structuresLinks
Brugia malayi8,743WormBase Parasite example
Caenorhabditis elegans19,694WormBase ParaSite example
Dracunculus medinensis10,834WormBase ParaSite example
Onchocerca volvulus12,047WormBase ParaSite example
Schistosoma mansoni13,865WormBase ParaSite example
Strongyloides stercoralis12,613WormBase ParaSite example
Trichuris trichiura9,564WormBase ParaSite example
Wuchereria bancrofti12,721WormBase 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?
The page containing the 3D protein structure for a protein of interest is located under the transcript summary page on the left-side “Transcript-based displays” menu under “AlphaFold predicted model”. For a step-by-step tutorial click here. You can now view the shiny new interactive 3D AlphaFold structure for our protein of interest:

AlphaFold predicted model page for S. mansoni transcript Smp_170450.1 in WormBase ParaSite 17

“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 then be able to enable “AlphaFold predicted model” viewer for these species. You can monitor the list of species present in the AlphaFold database here.


Phenotypes available on the FTP

“Is there any way to export gene-phenotype associations from WormBase ParaSite?”

In our previous release 16 we were happy to announce the import of over 350,000 C. elegans and S. mansoni gene-phenotype associations from our sister site, WormBase (C. elegans example). These associations were also propagated between orthologs to all our hosted species (H. polygyrus example). In this release we also made these gene-phenotype associations available in our FTP directory.

Gene-Phenotype associations have been deposited in GAF version 2.1 files in our FTP directory. For each species you will find 2 different GAF files:

  1. <SPECIES>.<BIOPROJECT>.WBPS17.orthology-inferred_phenotypes.gaf.gz (Example): This file contains species-specific orthology inferred gene-phenotype associations from C. elegans or S. mansoni (you can find which one in the 8th column). A file like this is availabe for every species in WormBase ParaSite.
  2. <SPECIES>.<BIOPROJECT>.WBPS17.phenotypes.gaf.gz (Example): This file contains original gene-phenotype associations for the species of interest. For the moment we only host original gene-phenotype association data for C. elegans and S. mansoni and therefore this file is available for these 2 species.

Sometimes GAF files are hard to interpret. For this reason, in the header of these files, we have included very useful column descriptions and general information. Enjoy!

Curated gene synonyms

“Gene synonyms are really useful, but is there any way to export them?”

In our release 16 we announced the import of literature-curated gene name synonyms for Strongyloides stercoralis. These synonyms are searchable (via the top-right search box) and appear in the new “Synonyms” line of the gene page. In this release we also made these synonyms exportable via WormBase ParaSite Biomart!

To export curated gene synonyms for S. stercoralis: First navigate to the WormBase ParaSite Biomart and submit your Query Filters. Then enable the “Curated Gene Synonym ID” under the “EXTERNAL DATABASE REFERENCES AND ID CONVERSION” of the Output Attributes like shown here:

Then click Results and you will get a list of your selected genes and their curated synonyms:

We need your help on this!
At the moment, we have only imported External Curated Gene synonyms for S. stercoralis but we would love to import more synonyms for other species. For this reason we need your help! If you have (or someone you know has) curated gene synonyms for any of the genomes we are hosting in WormBase ParaSite please contact us (parasite-help@wormbase.org) and we will be able to integrate them.

Community Annotation

“I would like to manually curate gene models on a genome I have previously submitted (or I am about to submit) to WormBase ParaSite.”

We supplement our in-house gene curation platform by hosting Web Apollo instances for an increasing number of genomes. Web Apollo is an instanteneous, collaborative genomic annotation editor available on the web.
Users can request relevant Web Apollo instances to be deployed from us. We would be happy to provide the relevant training! Please feel free to contact us (parasite-help@wormbase.org) to make such a request.

WormBase ParaSite is hiring

Got a passion for parasitic worm genomics? Join our team! We’re hiring a bioinformatician at University of Glasgow.

The succesfull applicant will work on a range of data analysis, data integration, curatorial and community-engagement activities for WormBase ParaSite. This will include driving annotation improvements within WB-PS by developing new workflows, and enabling updates from the research community.

The post is available either for an experienced bioinformatician or a less experienced bioinformatician that wants to further develop their skills.

For more information and to apply click here.

AlphaFold added new 3D protein structures of parasitic worms

The latest AlphaFold database update in January 2022, added three-dimensional (3D) structures of complete proteomes for 27 new organisms relevant to neglected tropical diseases and antimicrobial resistance including 7 parasitic worms from WormBase ParaSite.

Determining the three-dimensional (3D) structure of a protein has been a computational challenge for decades, and can provide essential insights into the underlying mechanisms of the proteins’ functions. AlphaFold is an AI system, created in partnership between DeepMind and the EMBL-European Bioinformatics Institute (EMBL-EBI), that makes state-of-the-art accurate predictions of a protein’s structure from its amino-acid sequence. Launched in July 2021, the database initially released ~350,000 3D structures of the human proteome and other 20 biologically-significant organisms such as C. elegans, E. coli, fruit fly, mouse, zebrafish, malaria parasite and tuberculosis bacteria.

AlphaFold’s latest release, announced on the 28th January 2022, focused on organisms with a UniProt reference proteome that are relevant to Neglected Tropical Disease or antimicrobial resistance. The selection of 27 new species was based on priority lists compiled by the World Health Organisation and included 7 parasitic worms (Table 1). AlphaFold predicted these structures based on their Uniprot reference proteomes, provided through WormBase ParaSite.

SpeciesPredicted structuresLinks
Brugia malayi8,743WormBase Parasite, AlphaFold
Dracunculus medinensis10,834WormBase Parasite, AlphaFold
Onchocerca volvulus12,047WormBase Parasite, AlphaFold
Schistosoma mansoni13,865WormBase Parasite, AlphaFold
Strongyloides stercoralis12,613WormBase Parasite, AlphaFold
Trichuris trichiura9,564WormBase Parasite, AlphaFold
Wuchereria bancrofti12,721WormBase Parasite, AlphaFold
Table 1.Structural predictions for complete proteomes of parasitic worms in AlphaFold DB v.2.1.2

As the majority of helminth proteins do not currently have data from direct protein characterisation studies, the prediction of their 3D structures will provide researchers with a powerful tool in predicting their mechanisms of function and their role within the cell. Scientists can also develop in silico screening assays against drugs that work with the protein’s unique shape.

Figure 1. AlphaFold predicted 3D structure of Schistosoma Mansoni’s Malate dehydrogenase. You can find it here.

The database is expected to grow further in 2022 and cover additional proteomes, as well as a much larger proportion of all proteins in Uniprot (UniRef90).

If you cannot find the AlphaFold predicted structure for the protein of interest of your favourite worm, here are some suggestions:

  • Multiple isoforms are not covered in AlphaFold DB, so make sure you are using the most appropriate protein from the reference proteome of your species.
  • Try searching by protein or gene name rather than specific UniProt accession.
  • Check if your protein is in the reference proteome of one of the covered organisms or in Swiss-Prot.
  • Proteins with high sequence similarity will most likely have identical 3D structure predictions. If you don’t see the sequence you are looking for, try searching for it using the EBI Protein Similarity Search tool against the sequences in the AlphaFold DB and/or using the WormBase ParaSite BLASTp tool against species which already have their proteins in the AlphaFold database. If the query sequence is not available then a structure prediction with a similar sequence to the query may be available.
  • Contact us! If your favourite species or protein is not available yet, keep watching for further announcements (EMBL-EBI news, EMBL-EBI Twitter, DeepMind Twitter) , or let us know.

Undoubtedly, AlphaFold opens new research horizons and we would like to encourage our users to go and explore this ground-breaking dataset (https://alphafold.ebi.ac.uk/) by searching and testing the 3D protein models of your favourite worm. Over time, we are planning to create a deeper integration of this dataset into WormBase ParaSite, so it will be easier to search, analyse and interpret.

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@sanger.ac.uk).