Victor Klein-Sousa

Had a fantastic time at the first Danish Viruses of Microbes meeting! Great to see all the cutting-edge phage research in the Nordics. Honored to present RBPseg + the #tailfiber structural atlas. Thanks for the great questions & feedback! #DKVoM25 #Phages

RBPseg: Toward a complete phage tail fiber structure atlas pubmed.ncbi.nlm.nih.gov/40479047/ #cryoEM

This came at a great time, as I'll be presenting it at #DanishVOM
tomorrow morning. Looking forward to seeing many of you there.

Thanks again to the co-authors @aritz-roa.bsky.social
Claudia Kielkopf, Nicholas Sofos & Nicholas M. I. Taylor.

GitHub - VKleinSousa/RBPseg: RBPseg: A Tool for Tail Fiber Structure Prediction RBPseg: A Tool for Tail Fiber Structure Prediction - VKleinSousa/RBPseg

You can explore the RBPseg code here:

github.com/VKleinSousa/...

We’ve also added a module to classify new fibers, and a validation model to help assess prediction reliability - going beyond standard AlphaFold metrics.

RBPseg: Toward a complete phage tail fiber structure atlas RBPseg enables accurate modeling of tail fiber structure, providing the first comprehensive tail fiber structure atlas.

Excited to see our work published in @ScienceAdvances
!

We present RBPseg, a method for structural prediction of #phage receptor-binding proteins.

We applied it to diverse tail fibers and validated the predicted structures using #cryoEM.

Read here: www.science.org/doi/10.1126/...

I'm looking for a postdoc in computational evolutionary phage genomics, with the goal to better understand how protein innovation arises in viruses, at @jagiellonskiuni.bsky.social in Krakow (Poland).

Drop me a line if it sounds cool!

Deadline: 20.06.

Link here:
mcb.uj.edu.pl/documents/15...

GitHub - VKleinSousa/ProtCNet Contribute to VKleinSousa/ProtCNet development by creating an account on GitHub.

You can find the git here: github.com/VKleinSousa/...
and the notebook here: doi.org/10.5281/zeno...

I’ve been exploring interactive networks to visualize #protein structure contacts — super helpful for large viral complexes. I put everything together in a Google Colab in case it helps others too.
Here’s how it looks for the phage T4 baseplate:

Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social

Gp38 adhesins of Straboviridae phages recognize specific extracellular loops of outer membrane protein receptors - npj Viruses npj Viruses - Gp38 adhesins of Straboviridae phages recognize specific extracellular loops of outer membrane protein receptors

I'm happy to see that our collaboration is out on npj viruses! I had a fun time modelling T-even #phages adhesin proteins. Verifying that we can use #AF2 bias to select true binders was even cooler. Congrats to Veronika Lutz and all www.nature.com/articles/s44...

Have you checked the PHAGE journal? One of their manuscript types is called 'Bacteriophage Introduction'. And it sounds like what you're aiming for: home.liebertpub.com/publications....

Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states. Contractile injection systems (CISs) are phage-tail-like nanosyringes that mediate bacterial interactions by puncturing target cell membranes. Within these systems, Photorhabdus Virulence Cassettes (P...

🚨Super happy to see this preprint out!! Main part of Leyre’s PhD journey on the eCIS from Photorhabdus luminescens. Full structure using #cryoEM Check it out! 🎊

www.biorxiv.org/content/10.1...

LoVis4u: a locus visualization tool for comparative genomics and coverage profiles Abstract. Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task

Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...

🧵 on our preprint: Zhang & Skolnick's TM score for comparing model of protein to experimental structures of same protein. The d_j are essentially the same as the aligned error in Alphafold. After any structure alignment, it's the displacement of model Calpha from experimental Calpha of residue j.

It looks awesome, great work!

🚨 🧬 Updated preprint on the completed BASEL collection - what's new? Some fun with bacterial immunity and a new P22 relative infecting E. coli K-12. A thread 🧵

That's pretty cool! I’ve always wondered why more phages don’t have RBPs on their capsids - great to see them interacting with cryoET. I’m curious to see what types of adaptors these fibers have and how abundant they are. Great work :)

Kiwa is a bacterial membrane-embedded defence supercomplex activated by phage-induced membrane changes Bacteria and archaea deploy diverse, sophisticated defence systems to counter virus infection, yet many immunity mechanisms remain poorly understood. Here, we characterise the Kiwa defence system as a...

Happy to share our latest findings on Kiwa. Foundational work from Thomas, with Zhiying and Yi providing beautiful structures and molecular insights. Ever grateful for the collaborations with Eugene and Dinshaw. More to come 🙃 doi.org/10.1101/2023...