Structure of riboflavine
Periodic reminder that the fluorescent compound in mammalian cell culture media, such as DMEM, is riboflavin (not phenol red)
14.10.2025 19:51
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Structure of riboflavine
Periodic reminder that the fluorescent compound in mammalian cell culture media, such as DMEM, is riboflavin (not phenol red)
I’m biased 🇩🇰, but this is quite nice to read:
I thought science hinged on prestige. Moving abroad made me reassess my priorities
www.science.org/content/arti...
Speak up to prevent a major loss for the field. CASP, which helped shaping structural biology including AlphaFold is on the verge of shutting down. NIH funding has lapsed, UC Davis support ends and the core team is being let go. Painfully shortsighted.
Budget released today:
40% cut to NIH
50% cut to NSF
If enacted, this will destroy academic research in the United States. It will also have a major trickle down effect on the entire academic ecosystem
Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1...
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Small proteins can be more complex than they look!
We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
Just got an email from the Fulbright Association. As of right now, funding has been cut off to 12,500 US citizens currently abroad and and more than 7,400 foreigner scholars and students in the United States
Adding the relevant feeds
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#chemsky
#chembio
#chemicalbiology
My group is working within chemical biology, protein design, and biophysics. It would be great to be added to the science feed:
The ideal candidate has a solid foundation in experimental protein science. Additionally, experience with computational protein design or modeling is advantageous.
Our research group at Aarhus University integrates computational and experimental approaches within a multidisciplinary program aimed at creating, analyzing, and utilizing light- and ligand-controlled protein tools for studying biological processes.
We are looking for a postdoc with an interdisciplinary drive to join our team at Aarhus University. The project, funded by the Villum Foundation, focuses on leveraging recent advances in de novo protein design to develop novel photoactive proteins.
Are you serious @royalsociety.org?? He is trying to destroy science, spreading dangerous misinformation, inciting violence & your response is to do nothing?
So what’s your purpose then? What do you exist for? Other than being elite?
🧪 #academicsky
www.theguardian.com/technology/2...
Hey #chemsky and beyond, with all that is going on, I am curious what expensive, high margin molecules we could provide to the community for free. What things do you use all the time, cost way too much, and would make a difference? Alexa Fluor 488 NHS? Other dyes? Other molecule?
Instruktøren for kryolit-dokumentaren tager til genmæle i P1 Orientering - men svarene er langt fra overbevisende: www.dr.dk/lyd/p1/p1-or...
For mig at se er dokumentaren et eksempel på misinformation, som det oftest praksiseres i politik og på sociale medier.
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Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!
www.biorxiv.org/content/10.1...
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Special Bluetorial: The benefits of different life experiences
The scientific community has folks with a very wide range of life experiences. We have a lot to learn from one another.
New preprint from our group! We propose SHAPES, a set of metrics to quantify the distributional coverage of generative models of protein structures with embeddings at different structural hierarchies and quantify undersampling / extrapolation behaviors.
Yes it's important people understand a preprint hasn't been peer-reviewed. BUT it's also important to understand that what "peer-reviewed" means varies considerably, in some cases signifying nothing... www.science.org/content/arti...
A solid way to store FPs in my experience. But 30 years is impressive.
Aside from the fact that I love Doritos, Cheetos, and all snacks unnaturally orange, I appreciate the physics and potential impact on optical imaging of this paper:
www.science.org/doi/10.1126/...
A timeline titled "The Golden Age of Antibiotics" shows when each antibiotic drug class was first available for medical use, with example antibiotics labeled. Classes are color-coded by their source: actinomycetes, other bacteria, fungi, or synthetic. Milestones include the first antibiotics (arsphenamines in 1910), as well as the discovery of many actinomycetes-derived antibiotics, such as streptomycin, and sulfonamides, penicillins, and tetracyclines. Data: Hutchings, Truman, Wilkinson (2019). Created by Saloni Dattani for Our World in Data.
Many people talk about the "Golden Age of Antibiotics", but I hadn't seen it visualized properly.
Just how many types of antibiotics were discovered during that time?
So, I visualized it myself!
1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens
TRACeR for MHC-I: go.nature.com/4gcLzn5
TRACeR for MHC-II: go.nature.com/4gj5OQk
Back by popular demand, I present PPI Prediction Challenge #2.
My claim: I AM SKEPTICAL COMPUTATIONAL APPROACHES CAN PREDICT WHETHER TWO PROTEINS INTERACT.
Someone prove me wrong (take two).
docs.google.com/forms/d/e/1F...
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You may have seen a recent pre-print [1] from Jain et al. with strongly worded claims against the experimental results in our DiffDock paper [2]. We initially declined to respond as we saw that this preprint contained falsehoods, misleading comparisons, seemingly deliberate omissions, ...1/n
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
Hey @biorxivpreprint.bsky.social, I think you need to add another icon here 🦋
PIONEERS
When I assumed the position as Director of NIGMS in 2003, Dr. Zerhouni's project for stimulating activities across NIH, The NIH Roadmap for Medical Research, was under active development. The Roadmap included a range of different funding opportunities.
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www.science.org/content/arti...
Protein engineering details, chromatography profiles and spectroscopic characterization
Photocycle details and structural data
We engineered bacteriorhodopsin to be soluble. It binds retinal and can photocycle! X-ray structure reveals conserved binding pocket with 0.8 Å all atom RMSD to WT BR. All this became possible due to hard work by Andrey Nikolaev and the team 🙏 #proteindesign biorxiv.org/cgi/content/...
Crosspost from X: After showing that AF2 can be used to design very large proteins by performing #RSO, I am happy to share another fun project we did: the #af2cycler @sokrypton.org @hendrikdietz.bsky.social
www.biorxiv.org/content/10.1...
