Ulad Litvin
@ulad-litvin.bsky.social
92 followers 140 following 7 posts
PhD student (MRC-UofG CVR) 🏰 antiviral defence | 🧬 evolution | 🔮 protein structure prediction
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ulad-litvin.bsky.social
Thank you for the kind words, Joe. This was a team effort and I’m grateful for being part of it. Such an incredible experience 🤩
ulad-litvin.bsky.social
🌊 Coronaviruses likely acquired their spike proteins from aquatic herpesviruses. 4/5
ulad-litvin.bsky.social
🔍 Searches against structural network are extremely sensitive and allow to recover more RdRps than iterative profile-based searches. 3/5
ulad-litvin.bsky.social
🦠 The diversity of viral proteins can be reduced to 19,000 structural clusters. A structure-similarity network captures relationships between them. 2/5
Reposted by Ulad Litvin
grovearmada.bsky.social
🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses.

🔗 viro3d.cvr.gla.ac.uk
📄 www.embopress.org/doi/full/10....

@molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠
Viro3D
viro3d.cvr.gla.ac.uk
Reposted by Ulad Litvin
zaminiqbal.bsky.social
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Reposted by Ulad Litvin
Reposted by Ulad Litvin
kranzuschlab.bsky.social
How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense

www.biorxiv.org/content/10.1...
Reposted by Ulad Litvin
multicellgenome.bsky.social
More on the ancient foundation of animal development. Coyle & King illustrate how core regulatory modules were present in our pre-animal ancestors. The key was not invention, but recycling & new protein interactions. #CellBiology #multicellularity #protistsOnSky
www.nature.com/articles/s41...
Reposted by Ulad Litvin
cpuentelelievre.bsky.social
#structuralphylogenetics #strphy #3di
Reposted by Ulad Litvin
grovearmada.bsky.social
Some excellent lunchtime reading right here from @jonathonmifsud.bsky.social 👇

Lots to be learned about the origins & evolution of viruses by integrating sequence AND structure.

Work to be done to develop best-practices, but I expect we'll be seeing much more of the viral family-tree(s) soon.
Reposted by Ulad Litvin
mkrupovic.bsky.social
Check out our paper in PLoS Genetics with @umbertorosani.bsky.social and Marco Gerdol on the highly dynamic pangenome of basal chordates. It is enriched in defence and immunity genes (like in prokaryotes) and follows Mendelian inheritanceis rules. @plos.org journals.plos.org/plosgenetics...
Reposted by Ulad Litvin
ncorley.bsky.social
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)

[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Accelerating Biomolecular Modeling with AtomWorks and RF3
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...
www.biorxiv.org
Reposted by Ulad Litvin
bejalab.bsky.social
A novel mobile genetic element with virus-like characteristics is widespread in the world's oceans www.biorxiv.org/content/10.1...
Reposted by Ulad Litvin
fnobrega.bsky.social
Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription.

www.cell.com/cell/fulltex...

Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.
Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites
Zhang, Todeschini, and Wu et al. show that the bacterial defense system Kiwa senses phage attachment at the membrane and assembles a transmembrane complex that halts infection by blocking phage DNA re...
www.cell.com
Reposted by Ulad Litvin
nitzantal.bsky.social
📢Preprint out!
Excited to share my final work from the @soreklab.bsky.social!

We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.

Found 3 new families targeting immune signaling!
Reposted by Ulad Litvin
franknoe.bsky.social
BioEmu now published in @science.org !!

What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
Reposted by Ulad Litvin
martinsteinegger.bsky.social
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Reposted by Ulad Litvin
erinharvey.bsky.social
Got a great idea for a metagenomic virus discovery project but not sure what to do next? We are running a 5 day hands on workshop in beautiful Stellenbosch, South Africa with experts from around the world. Applications are open until 31st July. climade.health/2025/06/22/m...