FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
The real drama of life happened "backstage" in the unicellular world. 🎭🧬 #protistsonSky
Our postdoc Vika Shabardina is co-organizing this symposium with Annia (@ankarn.bsky.social). Two brilliant minds leading the evocell way!
Plus, a talk by @vikramalva.bsky.social. 👇
We envisioned pLAST as a BLAST-like tool, but tailored for plasmid sequences. pLAST can be run online (plast.lbs.cent.uw.edu.pl) or locally (github.com/labstructbio...) to search, classify and explore plasmid diversity. We would greatly appreciate your feedback! ➡️ www.biorxiv.org/content/10.1...
"Exclusive: Medical journal rejects Kennedy's call for retraction of vaccine study"
I got followed by exactly the same dog from two different accounts. Are fake accounts becoming a problem on BS?
▓▓▓▓▓▓▓▓▓▓▓░░░░░░░░░ 59.86%
It should also be illegal to force cats to wear collars with bells :)
▓▓▓▓▓▓▓▓▓▓▓░░░░░░░░░ 58.49%
a fire truck's diesel engine?
A 6-year internship? that’s something! ;)
I am #exhilarated to share that our new paper "LIGYSIS-web: a resource for the analysis of protein-ligand binding sites" is now published in @narjournal.bsky.social! After almost two years of development and more than 600 commits, LIGYSIS-web is out!
📜 : tinyurl.com/utges-LIGYSI...
We are pleased to announce that the next speaker in the ProSE seminar series will be Dr. Klara Hlouchova with a talk on "Protein Structure Before LUCA"
May 13, 4PM CET
Registration link: tinyurl.com/prose-seminar4
Please share!
We have benchmarked the AF2 multimer on coiled-coil domains and the results are also very good (even outperforming dedicated tools). Interestingly, the performance does not depend on the use of MSA: onlinelibrary.wiley.com/doi/full/10.....
This chopped alignment does not look meaningful. Or do I miss something?
Coiled coils (CCs) are protein domains in which alpha helices assemble into regular supercoiled bundles. In our new paper, we investigate how accurately AlphaFold2 predicts the oligomeric state, topology, and fine structural details of CC domains: onlinelibrary.wiley.com/doi/10.1002/....
Large livestock facilities in states across the country have become epicenters of bird flu, and some researchers say that’s no surprise:
Putting thousands of animals together in confined, cramped barns or corrals creates a petri dish for virus to spread, according to WIRED.
Maybe “Logicomix: An epic search for truth”?
If talent and opportunity were equally distributed, the average #NobelPrize winner would come from a middle income background.
The reality? The average laureate grew up in a household just below the top 10%. More than 50% come from the top 5%.
🧪🎩💰
www.theguardian.com/commentisfre...
New @science.org
from my Scripps Research colleagues on H5N1
A single mutation can increase the virus's binding to human receptors, highlighting the need for rigorous surveillance
science.org/doi/10.1126/...
Figure from Vita et al., 2016, Sci Rep: https://www.nature.com/articles/srep39065
I have a PhD position available in my group, to start in March 2025. If you have a keen interest in biochemistry and would like to study an exciting and novel class of copper proteins (aka weird Cu tubes) from bacteria, I'd love to hear from you.
You should apply here: ibb.edu.pl/app/uploads/...
We’ve seen such cases among coiled-coil domains. Fig. 8 here www.biorxiv.org/content/10.1...
Related to that, there is a fun PPI prediction challenge by @chembiobryan.bsky.social, which I'd like to advertise to everyone developing PPI prediction models. Tests like that are crucial for assessing model generalization capabilities!
www.dickinsonlab.uchicago.edu/ppi-challenge
"If only there was some way to remove viruses from milk" - it's easy, just drink plant-based milks :)
Not only is this an illusion, but it is a western culture-oriented illusion.
Left, cry-EM structure of the complex between MIK2 (green), the immunoregulatory peptide SCOOP (yellow) and the LRR of the co-receptor BAK1 (white) with only the most rigid part of the N-glycans resolved (1 or 2 or none) and represented with sticks. Right, reconstruction of the N-glycosylation with plant N-glycans G90477LS,selected to be all the same as glycoproteomics data is not available (as far as I know)
If you are interested or working in #structuralbiology, as you see any protein (yes, *any*), you should be thinking: is it glycosylated? The answer is likely to be yes! You can predict N-glycosylation sites and rebuild all types of glycans with ReGlyco glycoshape.org 😌
Check out the example ⬇️ 1/2
How do you study a family of protein domains whose function depends on their dynamics? Let's model 5000 homologs with AlphaFold2 and see what happens. The case of dimeric HAMP domains of prokaryotic signal transduction proteins: onlinelibrary.wiley.com/doi/full/10....
Our paper looking into the phenomenon of domain mosaicism in phages is now out in Nature Communications. Work led by Bogna Smug together with Krzysztof Szczepaniak, @epcrocha.bsky.social and @staszekdh.bsky.social. See a short thread. 1/7
www.nature.com/articles/s41...
