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Gabriel Oka

@okagu.bsky.social
45 followers 62 following 7 posts
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Gabriel Oka @okagu.bsky.social · 28/08/2026
A while ago, I was asked how I would teach the next generation of researchers to identify protein–protein interaction networks in unexplored bacterial genomes. I still don’t have the answer. ppigFinder is one attempt to move toward it, a fantastic collaborative effort within the CEPID B3 network.
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Gabriel Oka @okagu.bsky.social · 28/08/2026
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Gabriel Oka @okagu.bsky.social · 28/08/2026
🧬 Happy to share our new preprint: ppigFinder, a desktop tool integrating bacterial genome analysis with large-scale AlphaFold 3 protein–protein interaction screening. We showcase it by exploring the VirD4 interactome of Xanthomonas citri. 💻 github.com/leepusp/ppig...
github.com
GitHub - leepusp/ppigfinder
Contribute to leepusp/ppigfinder development by creating an account on GitHub.
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Gabriel Oka @okagu.bsky.social · 28/08/2026
www.biorxiv.org/content/10.6...
biorxiv.org
ppigFinder: an integrated desktop application for bacterial genome annotation and AlphaFold 3 based protein protein interaction screening
Motivation. AlphaFold-based structure prediction has transformed structural biology by enabling accurate protein modelling and providing a powerful framework for inferring protein-protein interactions...
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Reposted by Gabriel Oka
cryoEM papers @cryoempapers.bsky.social · 27/08/2026
ppigFinder: an integrated desktop application for bacterial genome annotation and AlphaFold 3 based protein protein interaction screening www.biorxiv.org/content/10.64898/2026.08.23.746524v1 #cryoEM
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Gabriel Oka @okagu.bsky.social · 15/07/2026
Very interesting work. Congratulations to the authors!
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Reposted by Gabriel Oka
Rémi Fronzes @fronzeslab.bsky.social · 26/05/2026
New preprint. In S. sanguinis, a C5a peptidase-like protease (ScpH) polymerizes along eDNA, turning it into a catalytic biofilm scaffold. Great work from @robinanger.bsky.social in our lab, with Pelicic lab @lcbofficiel.bsky.social www.biorxiv.org/content/10.6...
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Gabriel Oka @okagu.bsky.social · 11/05/2026
Happy to share our new bioRxiv preprint: “To Kill or not to Kill: A Conserved Trans-Intoxication Protection Factor Blocks X-T4SS-Mediated Fratricide through Interaction with VirB5” www.biorxiv.org/content/10.6...
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Gabriel Oka @okagu.bsky.social · 18/07/2025
Congratulations on the preprint! Thanks for sharing this refreshing and intriguing concept in interbacterial antagonism. An important piece in the puzzle of the underexplored role of immunity proteins.
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