If you are into plasmid research, try pLAST. By representing plasmids as ORF chains, it enables fast searches of 700k PlasmidScope sequences in global (find similar plasmids) or local (find recurring gene modules) mode. Available as server or local package. Feedback welcome! Links below ⬇️

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...

Multiple protein structure alignment at scale with FoldMason

Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

science.org

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. 👇

Society for Molecular Biology and Evolution@official-smbe.bsky.social · 8mo ago

Organisers - Victoria Shabardina | @ibe-barcelona.bsky.social - @ankarn.bsky.social | University of Warsaw Invited Speaker - @vikramalva.bsky.social | @mpi-bio-fml.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"

Exclusive: Medical journal rejects Kennedy's call for retraction of vaccine study

An influential U.S. medical journal is rejecting a call from Health Secretary Robert F. Kennedy Jr. to retract a large Danish study that found that aluminum ingredients in vaccines do not increase health risks for children, the journal's editor told Reuters.

reuters.com

I got followed by exactly the same dog from two different accounts. Are fake accounts becoming a problem on BS?

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▓▓▓▓▓▓▓▓▓▓▓░░░░░░░░░ 58.49%

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!

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.

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...

The science behind winning a Nobel Prize? Being a man from a wealthy family | Torsten Bell

A lot of talent is wasted in a world where more than half of laureates come from households in the richest 5%

theguardian.com

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/...

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/...

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 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...

Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with ...

Proteins are composed of distinct functional domains, each serving a specific role. Here, Smug et al. show that phages are able to shuffle fragments of their proteins and this predominantly occurs in ...

nature.com