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Protein Cosmos

Protein Cosmos

by Kate Michie Kate Michie

Feed for scientists interested in all aspects of Protein Science- think structural biology, biophysics, mass spec. (follows posts with cryoEM structural biology, alphafold, biophysics). tag with 🧬🧶

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  • 💙 Liked by 93 users
  • 📅 Updated 3 months ago
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Computational and Structural Biotechnology Journal (CSBJ)
@csbj.org
28 minutes ago
🔗 Predicting PROTAC off-target effects via warhead involvement levels in drug–target interactions using graph attention neural networks. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.cs... 📚 CSBJ: www.csbj.org #StructuralBiology #ChemicalBiology #PROTAC #DrugDiscovery
Predicting PROTAC off-target effects via warhead involvement levels in drug–target interactions using graph attention neural networks. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.028
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Jonathan Rosenblum
@jsrosenblum.bsky.social
about 2 hours ago
Reminder: Your enzyme having that name DOES NOT mean that's all it does. Metabolic enzymes like PGDH have a bunch of substrates and the enzyme is usually named for the first and/or easiest to assay. Regardless, cool report on a cool drug target #chemsky #chemchat
Inhibition of 15-hydroxy prostaglandin dehydrogenase promotes cartilage regeneration

www.science.org

Inhibition of 15-hydroxy prostaglandin dehydrogenase promotes cartilage regeneration

Aging or injury to the joints can lead to cartilage degeneration and osteoarthritis (OA), for which there are limited effective treatments. We found that expression of 15-hydroxy prostaglandin dehydro...
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Computational and Structural Biotechnology Journal (CSBJ)
@csbj.org
about 2 hours ago
🔗 Temporal complexity of LVV-hemorphin-7 allosterism at the angiotensin II type 1 receptor assessed using entropy-based approaches. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.cs... 📚 CSBJ: www.csbj.org #StructuralBiology #Biophysics #GPCR #Entropy #Pharmacology
Temporal complexity of LVV-hemorphin-7 allosterism at the angiotensin II type 1 receptor assessed using entropy-based approaches. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.024
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Korostelev Lab
@korostelevlab.bsky.social
about 2 hours ago
Using "in extracto cryo-EM", we visualize ribosomes in mammalian lysates, including RRL. "Hibernating" ribosomes carry an extended set of proteins that protect functional centers. These include elongation factor eEF2, LARP1 implicated in mTOR signaling, eIF5A etc. www.biorxiv.org/content/1….
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cryoEM papers
@cryoempapers.bsky.social
about 2 hours ago
Precision mRNA Delivery via Ultrasound-Controlled Release Perfluorocarbon Emulsions: An Innovative Ultrasound Theranostic Strategy with 19F MRI Feasibility pubmed.ncbi.nlm.nih.gov/4… #cryoEM
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Sjors Scheres
@sjorsscheres.bsky.social
about 5 hours ago
The #cryoEM field perhaps went a little astray with overfitting pre-revolution, and a few individuals fell into the Einstein-from-noise trap. But overall, big deviations from progress have been avoided.
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cryoEM papers
@cryoempapers.bsky.social
about 5 hours ago
Chemical Mechanism of Allosteric and Asymmetric Dark Reversion in a Bacterial Phytochrome Uncovered by Cryo-EM pubmed.ncbi.nlm.nih.gov/4… #cryoEM
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whygavs
@whygavs.bsky.social
about 5 hours ago
This is using machine learning to build a neutral network to make predictions based on a huge dataset. Similar to what Google shared a Nobel Prize for with protein design.
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RCSB Protein Data Bank
@rcsbpdb.bsky.social
about 5 hours ago
AI-Designed Antibodies Achieve Atomic Precision to Enhance Drug Discovery
AI-Designed Antibodies Achieve Atomic Precision to Enhance Drug Discovery

www.genengnews.com

AI-Designed Antibodies Achieve Atomic Precision to Enhance Drug Discovery

David Baker’s Nobel Prize winning lab has generated antibodies from scratch that target user-specified binding sites for AI therapeutic design.
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Jaan Mannik
@jaanmannik.bsky.social
about 6 hours ago
📢Our MD simulation is out in Biophysical Journal! The nonequilibrium polysome dynamics expands bacterial nucleoids and helps separate daughter chromosomes. Results agree with our previous experiments and extend our earlier model. authors.elsevier.com/a/1m…. #Microbiology #Biophysics
Snapshot of a model showing two chromosomes (red spheres on the left and yellow ones on the right) before they are fully separated. Kymographs (bottom row) show the density of two daughter chromosomes (left) and ribosomes (right) as a function of time in the presence of nonequilibrium reactions of ribosomes. Blue corresponds to low and red to high density. As time progresses, the two chromosomes separate, but only when the reactions are present. The snapshot above corresponds to time t = 0 in the kymographs.
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Andrea Musacchio
@andrea-musacchio.bsky.social
about 6 hours ago
You could probably explain this with an analogy. A protein crystal, and the theory that defines how you explain what's inside. Bragg's low uses an incorrect analogy (planes in crystals that reflect X-rays) and its use is limited. Fourier transform provides a literal description and is powerful.
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SkynetAndChill.com
@skynetandchill.com
about 7 hours ago
DeepMind's transformer-based AlphaFold 2 predicted protein structures to near-atomic accuracy in hours, DeepMind has released roughly 200 million protein predictions, and co-leads John Jumper and Demis Hassabis won the 2024 Nobel Prize in Chemistry.
What’s next for AlphaFold: A conversation with a Google DeepMind Nobel laureate

www.technologyreview.com

What’s next for AlphaFold: A conversation with a Google DeepMind Nobel laureate

“I’ll be shocked if we don’t see more and more LLM impact on science,” says John Jumper.
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TJ McCorvie
@allostericstate.bsky.social
about 7 hours ago
www.biorxiv.org/content/1…. Example of Relion Blush regularisation combined with CryoDRGN to overcome orientation bias issues from Teder et al #CryoEM
Screen shot of supplementary fig 2 from the bioRxiv preprint https://www.biorxiv.org/content/10.1101/2025.11.26.690380v1.abstract. It shows cryo-EM derived volumes using cryoSPARC NU refinement vs using Relion Blush regularisation and subsequent 3D classification using cryoDRGN to overcome orientation bias issues see in CS refinement.
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Xin Xiang
@xianglab.bsky.social
about 7 hours ago
Without these possibly impossible mutants, it is hard to falsify that LLPS may play a role somewhere in the process just as more specific protein-protein interactions. Both could be necessary (neither is sufficient). I have never worked on LLPS. These discussions are very helpful! Thanks!
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cryoEM papers
@cryoempapers.bsky.social
about 8 hours ago
Cryo-EM structure of drug-resistant Escherichia coli phage E1004 reveals a conserved cylindrical core among podophages pubmed.ncbi.nlm.nih.gov/4… #cryoEM
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Lars-Anders Carlson
@lacarlson.bsky.social
about 8 hours ago
Is LLPS the cell biologists' equivalent of the FSC discussions in cryo-EM? Recent threads on here make me think that.
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Ned Peyroux
@o0ned.bsky.social
about 8 hours ago
James DeMeo makes sense of Reich's later biophysical works, corroborating evidence with Reich's predecessors & contemporaries well as modern confirmation of his findings. Reich unified ether physics with terrain biology, & both are suppressed sciences, rendering orgone biophysics effectively taboo.
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disappeared by bluesky mods
@chemotaxis.bsky.social
about 9 hours ago
to the extent that "AI" has been really useful in my life it's been in applying it to data sets that are very large and that we don't intuitively understand (genomics, protein structure). it's weird to me that people keep making it try to write emails.

This is a legitimate scientific revolution in meteorology. Also, to be clear, these models are not the AI LLMs that most people are familiar with. They are machine learning algorithms trained on observations (actually reanalysis).

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Matthijs
@mccaine.bsky.social
about 9 hours ago
This is also why general ranting about "AI" is so unhelpful. I quite like protein structure prediction personally
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cryoEM papers
@cryoempapers.bsky.social
about 10 hours ago
Mechanistic insights into histone recognition and H3K14 acetylation by the NuA3 histone acetyltransferase complex pubmed.ncbi.nlm.nih.gov/4… #cryoEM
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Claudio Bussi
@claudiobussi.bsky.social
about 12 hours ago
Interested in an interdisciplinary PhD program at the intersection of cell biology, biophysics, and chemistry? Please check out the available projects at Nanyang Technological University Singapore IDMxS, and feel free to reach out if you are considering applying! idmxs.org/opportunitie...
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cryoEM papers
@cryoempapers.bsky.social
about 13 hours ago
Structural basis of sodium ion-dependent carnitine transport by OCTN2 pubmed.ncbi.nlm.nih.gov/4… #cryoEM
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Daniel Asarnow
@dabiophysicist.bsky.social
about 13 hours ago
In structural biology we say that when a validation measure becomes a refinement target, it's no longer a good validation measure. IMO you're getting at an analog that the more widely an assessment separates students (i.e. the better its signal), the less useful it is as a minimum qualification
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Netzschleuder
@netzschleuder.skewed.de
about 14 hours ago
drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster). Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. 2939 nodes, 8723 edges. networks.skewed.de/net/dr… Ridiculogram:
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cryoEM papers
@cryoempapers.bsky.social
about 15 hours ago
Bifunctional Architecture Enables Substrate Catalysis and Channeling in Paracoccus TMAO Demethylase www.biorxiv.org/content/1… #cryoEM
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