Ulad Litvin
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ulad-litvin.bsky.social
Ulad Litvin
@ulad-litvin.bsky.social
PhD student (MRC-UofG CVR)
🏰 antiviral defence | 🧬 evolution | 🔮 protein structure prediction
Pinned
Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵

📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...
doi.org
Reposted by Ulad Litvin
Reliable Identification of Homodimers Using AlphaFold https://www.biorxiv.org/content/10.1101/2025.11.27.691011v1
November 28, 2025 at 2:46 AM
Reposted by Ulad Litvin
Are you fascinated by viruses? Would you like to design your own original research project in the UK's largest virology centre? Why not come and do a PhD @cvrinfo.bsky.social - application deadline 6th Jan 2026 (1/1): www.findaphd.com/phds/program...
FindAPhD : The MRC-University of Glasgow Centre for Virus Research (CVR) PhD Funded Programme at University of Glasgow
Apply for a PhD: The MRC-University of Glasgow Centre for Virus Research (CVR) PhD Funded Programme at University of Glasgow
www.findaphd.com
November 27, 2025 at 1:26 PM
Reposted by Ulad Litvin
A few py2Dmol updates 🧬

py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
November 19, 2025 at 8:15 AM
Reposted by Ulad Litvin
Viro3D delivers >85,000 AI-predicted protein structures for >4,400 viruses, expanding viral structural coverage 30-fold, enabling new insights to virus function/evolution.
#VirusBioinformatics #StructuralBiology🧬🔍
📄 doi.org/10.1038/s443...
👤EVBC members: Spyros Lytras, David Robertson, Joseph Hughes
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...
doi.org
November 14, 2025 at 8:33 AM
Reposted by Ulad Litvin
Our November issue is available at journals.iucr.org/d/issues/202...

On the cover: recent studies demonstrate that the range of samples suitable for cryo-EM single-particle analysis is expanding towards increasingly more native samples. Read the review at shorturl.at/mitjg
November 5, 2025 at 1:29 PM
Reposted by Ulad Litvin
AI in Protein Design: Hype vs. Reality Explained by David Baker
In this GEN interview, he emphasizes that designing new proteins from scratch is now a reality. Whether AI transforms medicine will require improving our understanding of biology's complexity
AI in Protein Design: Hype vs. Reality Explained by David Baker
In this GEN interview, Nobel Laureate David Baker, PhD, emphasizes that designing proteins from scratch is reality and unpacks what's needed for AI to transform medicine.
www.genengnews.com
November 2, 2025 at 5:34 PM
Reposted by Ulad Litvin
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 26, 2025 at 10:40 PM
Reposted by Ulad Litvin
New preprint alert!! 🚨🚨🚨in collaboration with the Letko @fviromics.bsky.social and Baric labs!

Just in case you're tired of sarbecoviruses, this time we looked at ACE2-using merbecoviruses! specifically the first HKU5r-CoVs detected in mink a couple of years ago.

www.biorxiv.org/content/10.1...
Structural and phenotypic plasticity of the RBD loop2 region is a key determinant for HKU5r-CoVs’ emergence in mink
The emergence of novel coronaviruses from animal reservoirs continues to pose a significant zoonotic threat. Here, we investigate the evolutionary origins and virological properties of a recently repo...
www.biorxiv.org
October 28, 2025 at 5:07 AM
Reposted by Ulad Litvin
Our PLM-interact is out in Nature Communications! We show that jointly encoding protein pairs using protein language models improves protein–protein interaction prediction performance and enables fine-tuning to predict mutation effects in human PPIs. www.nature.com/articles/s41...
PLM-interact: extending protein language models to predict protein-protein interactions - Nature Communications
Protein structure can be predicted from amino acid sequences with unprecedented accuracy, yet the prediction of protein–protein interactions remains a challenge. Here, authors present a sequence-based...
www.nature.com
October 28, 2025 at 3:27 PM
Reposted by Ulad Litvin
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
Reposted by Ulad Litvin
Abstract submissions are open for #APSPM2026!
🗓️ Deadline: Nov 28, 2026
📍 Brisbane + online
🎓 Travel grants for students & ECRs
Join us to explore how protein structures and AI are reshaping evolutionary biology.

@official-smbe.bsky.social

#StrPhy26 #StrPhy
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
October 24, 2025 at 4:06 AM
Reposted by Ulad Litvin
My lab is hiring postdocs! We combine AI, protein structure prediction and comparison, and high-throughput virology to study the virus-host conflict.

You can read more about my lab's research here: jasonnomburg.com/research/

Apply here to join us in lovely Vienna! aithyra.onlyfy.jobs/job/0khkxp82
The Starting Principal Investigators at #AITHYRA the Research Institute for Biomedical Artificial Intelligence of the OeAW in Vienna invite outstanding candidates to apply for postdoctoral positions in the field of AI/ML & Life Sciences.
www.oeaw.ac.at/aithyra/post...
Please apply by 20 Nov 2025!
October 20, 2025 at 1:03 PM
Reposted by Ulad Litvin
Perfect timing in the field for a beautiful review on NAD+ in bacterial immunity by @hugovaysset.bsky.social and @audeber.bsky.social @cp-molcell.bsky.social

#MicroSky

www.cell.com/molecular-ce...
October 16, 2025 at 2:58 PM
Reposted by Ulad Litvin
The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition

By Dustin Glasner, Matthew Daugherty & colleagues.

#microsky

www.nature.com/articles/s41...
The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition - Nature Microbiology
Viruses generally have compact genomes, resulting in many viral mRNAs with short 5’ untranslated regions. An antiviral complex exploits this feature of viral mRNAs to selectively inhibit viral protein...
www.nature.com
October 15, 2025 at 4:59 PM
Reposted by Ulad Litvin
New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬

Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social

www.embopress.org/doi/full/10....
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...
www.embopress.org
September 28, 2025 at 5:39 AM
Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵

📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...
doi.org
September 26, 2025 at 2:06 PM
Reposted by Ulad Litvin
🚨 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
September 26, 2025 at 11:36 AM
Reposted by Ulad Litvin
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
September 25, 2025 at 9:29 PM
Reposted by Ulad Litvin
The mechanism of STING NF-κB signaling has remained a mystery. An exciting new study from the Paludan lab now uses data throughout animal STING evolution to provide new answers – including isolating white blood cells from turtles and carp!

www.nature.com/articles/s41...
STING signals to NF-κB from late endolysosomal compartments using IRF3 as an adaptor - Nature Immunology
Here the authors show how the DNA-sensing cGAS–STING pathway activates NF-κB and inflammatory gene expression with delayed kinetics via post-Golgi endolysosomal signaling.
www.nature.com
September 22, 2025 at 3:39 PM
Reposted by Ulad Litvin
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...
September 5, 2025 at 10:13 AM
Reposted by Ulad Litvin
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...
September 8, 2025 at 9:33 AM
Reposted by Ulad Litvin
August 22, 2025 at 12:20 PM
Reposted by Ulad Litvin
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.
August 26, 2025 at 11:47 AM
Reposted by Ulad Litvin
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...
August 18, 2025 at 10:30 PM
Reposted by Ulad Litvin
(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
August 15, 2025 at 5:17 PM