Victor Klein-Sousa
@vkleinsousa.bsky.social
PhD Fellow @cphbiosciphd @NMITaylorLab @UCPH_CPR 🇩🇰 | Structural biology 🤝 phages 🔬 🇧🇷 (he/him)
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
June 13, 2025 at 6:43 PM
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
Reposted by Victor Klein-Sousa
RBPseg: Toward a complete phage tail fiber structure atlas pubmed.ncbi.nlm.nih.gov/40479047/ #cryoem
June 7, 2025 at 10:27 AM
RBPseg: Toward a complete phage tail fiber structure atlas pubmed.ncbi.nlm.nih.gov/40479047/ #cryoem
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/...
!
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/...
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.
www.science.org
June 10, 2025 at 6:20 AM
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/...
!
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/...
Reposted by Victor Klein-Sousa
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...
Drop me a line if it sounds cool!
Deadline: 20.06.
Link here:
mcb.uj.edu.pl/documents/15...
May 20, 2025 at 7:52 AM
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...
Drop me a line if it sounds cool!
Deadline: 20.06.
Link here:
mcb.uj.edu.pl/documents/15...
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:
Here’s how it looks for the phage T4 baseplate:
May 19, 2025 at 7:49 AM
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:
Here’s how it looks for the phage T4 baseplate:
Reposted by Victor Klein-Sousa
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
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes https://www.biorxiv.org/content/10.1101/2025.05.14.653371v1
May 19, 2025 at 6:37 AM
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
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...
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
www.nature.com
April 28, 2025 at 1:41 PM
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...
Reposted by Victor Klein-Sousa
🚨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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
April 22, 2025 at 12:54 PM
🚨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...
www.biorxiv.org/content/10.1...
Reposted by Victor Klein-Sousa
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...
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
academic.oup.com
February 25, 2025 at 7:27 AM
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...
Reposted by Victor Klein-Sousa
🧵 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.
February 16, 2025 at 2:13 AM
🧵 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.
Reposted by Victor Klein-Sousa
🚨 🧬 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 🧵
February 6, 2025 at 6:05 AM
🚨 🧬 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 :)
Want to know more about a flegellotrophic phage with flexible capsid fibers? Check out our new preprint in collaboration with the wonderful Scharf lab!
Using cryogenic electron microscopy methods to gain insight into structure and initial host attachment of the flagellotropic bacteriophage 7-7-1 https://www.biorxiv.org/content/10.1101/2025.01.29.635402v1
January 30, 2025 at 9:02 AM
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 :)
Reposted by Victor Klein-Sousa
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...
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...
doi.org
January 24, 2025 at 10:08 AM
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...