Against my better instincts, I have written some notes on how human probability judgements work and what you should expect from surveys that ask people to guess what proportion of the population is transgender. I hope never to speak of this matter again

Must be fun for the editors currently juggling the Rfdiffusion2 peer review. "Uh, authors have you seen there is a very similar, supposedly better model out there? Oh wait, it's the same authors" Seriously, what's the point of reviewing papers anymore if we're now at <6 months update cycles 🧐

In the first seven days since I launched this new game, almost ten thousand people from 82 countries have played it. (Top cities so far: New York City, Zurich, Toronto, Chicago, Berlin, Vienna, Stockholm) What topics would you like me to add next? dataguessr.com

Premium newsletter: A 8500 word analysis of how everybody is losing money on gen AI, with some startups spending 100%+ of their revenue on compute. Even GPU providers are struggling, with years-long time horizons to break even, if profit is even possible. www.wheresyoured.at/why-everybod...

I often wonder whether all the folks flocking to (lured into?) longevity research are thinking about who and what this tech will actually benefit

Good to see @bsky.app has emerged as the social media platform of choice for science stuff arstechnica.com/science/2025...

I'm essentially unable to log into any websites run by Editorial Manager. I have 20 something different logins saved, with different usernames and passwords, for different journals. My password manager is useless, and I am at the point where every login requires a PW reset.

"The goal is to place in the top category for merit pay that year, a range that could be anything from zero to upwards of $75 per academic semester. There is no actual money available for merit this year, but we will still conduct the reviews. The merit is symbolic."

(1/7) Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3) [https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)

My biochemistry I class has an ongoing project known as “my enzyme is the coolest” in which the students compete for their enzyme to be selected as the SUNY ESF Enzyme of the Year. I am putting together my list of nominees for the students to pick from. Please comment with your nominations!

No matter how hard you try, you simply cannot guess the journal withe the highest “impact factor” in organic chemistry last year. Really. Nor will you guess many of the other “winners”:

Since search is dead, how soon do you think Google Scholar is headed for the Google Graveyard? I'm betting it's soon, and academia is NOT prepared

Fellow scientists, have u heard of Cluely yet? Do u have thoughts on how to deal with this tech [AI software that provides real time answers/hints while listening to your conversation, used to "cheat" in online interviews] Are on-site interviews the only way now? Will we stop hiring from overseas?

Nice containerization of AlphaFold, Boltz, and Chai, and calculation of metrics (including our ipSAE score for protein-protein interactions). www.biorxiv.org/content/10.1...

We think we can do binder discovery faster and better than anyone in the world - computational or experimental. Happy to be challenged. 2/n

Ultrahigh-Throughput Multiplexed Screening of Purified Protein from Cell-Free Expression Using Droplet Microfluidics pubs.acs.org/doi/10.1021/...

ChimeraX daily builds can predict binding affinity of small molecules using Boltz 2 on your Mac, Windows or Linux computer. www.rbvi.ucsf.edu/chimerax/dat...

Now that OpenCRISPR is in nature and rekindled the 'what's-a-novel-sequence' debate, I'm happy to share an app to check this, which I built for fun some time ago. fuerstlab.shinyapps.io/SeqNovelty/ quick 🧵

Food for thought here for anyone not working at TRUE atomic resolution…

A small reminder to all structural biologists around working on biomolecular complexes: please consider sharing your complexes as targets for CAPRI - AI has not solved all structure prediction problems and there are still challenges! See www.capri-docking.org/contribute/

🤔 How do proteins fold while they're still being made? As the main project in my PhD, I developed "Arrest Peptide Profiling" to record proteins folding with as they emerge from ribosomes in living cells 🦠 - with single codon resolution! @natcomms.nature.com‬ 🧵 1/6 #ProteinFolding

I am so incredibly excited to share our latest work, on the exploration of #RNA secondary structure ensembles and discovery of RNA regulatory structural switches in bacteria and human cells, just out in @natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)

Biologist folk (especially in evolutionary biology and/or ecology, but it don’t matter): Can you give me your favorite examples of trade offs in biology? Organism or system don’t matter. Primary literature or reviews preferred.

Has anyone had issues/troubles getting Glutamine synthetase to "work well?" I keep getting low conversions and can't seem to resolve this. Pretty frustrated/embarrassed. Alternatively, if you know a NON-enzymatic way to do this, I'd be very interested! I feel like it should be doable. #chemsky 🧪

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

I’m looking for classic papers in biochemistry for my Biochem I class this fall! Any suggestions are appreciated! We cover nucleotide structure and function; central dogma; protein structure and function; enzymology; and lipid structure and function. Mountain pic for attention.

A very quickly emerging problem not only in the US. We are not prepared for this, are we @erc.europa.eu et al

The number of ways in which AlphaFold can be hacked is truly infinite

I am so grateful that this paper is out! It so eloquently describes so many of the issues I've seen with a lot of AGI experimentation that concludes that LLMs are scheming, ill-intentioned, or malicious, and the chimp language metaphor is the cherry on the cake 🍰 arxiv.org/abs/2507.03409

You designed binders for your favourite protein and wish there was a way to experimentally screen them within 24h w/ only a set of pipettes and a plate reader? Check out our Cell-Free 2-Hybrid approach (CF2H) Full post: tinyurl.com/48cz5nb6 Preprint: www.biorxiv.org/cgi/content/...

Lots to agree but as -published under antiAI URL indicates agenda -one conclusion= "give (ppl like) us more $" indicates bias -the "progress is stalling" intro, likely written on device whose charger cable's chip is more powerful than a PC from 2000, indicates ignorance --> read with some scepticism

1/6 One of the key features of functional proteins is their inherent structural flexibility. In our recent work at #ICML, we introduce flexibility to protein structure design! More in a thread below. Code / Tutorial: github.com/graeter-grou... Poster: W-109, Thu 17 Jul 11 a.m. PDT — 1:30 p.m. PDT

Preprint alert! With #PFAS contamination becoming an environmental crisis, we dared to engineer natural defluorinases towards degradation of (un)natural organofluorides. How? Check out our robust growth-based selection platform here: www.biorxiv.org/content/10.1... thanks to @mayerlab.bsky.social !

Fantastic opportunity at my postdoc institute 👇If you have any questions about a TT, life in Cambridge, the LMB or the PNAC division feel free to reach out !

The animated visualizations on this site are 🚨 insane 🚨. Insane is, too, to think that the default medium of science communication remains the pdf 🤦🏼‍♂️

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

White text on white background instructing LLMs to give positive reviews is apparently now common enough to show up in searches for boilerplate text.

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.

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design! github.com/martinpacesa...

✨Cradle is hiring protein+ML researchers!✨ We operate ML for lab-in-the-loop lead optimization across all industries (pharma, synbio, ...), modalities (antibodies, enzymes, ...), properties (binding, activity, ...) We're a scaleup and already relied upon by 4 of the top 20 big pharma. Apply here!

1/At the #HoffmanLab lab meeting, we often have tech talks describing useful tools for other lab members. Since they might also prove useful for others, we've been posting almost every #HoffmanLabTechTalk for years. 🧪🧬💻

Springer-Nature launched a series of "Discover" journals that closely mimic MDPI titles -- sharing *identical* journal names, and likely similar business model. What is going on, and why researcher will - as always - fall for it? A 🧵 the-strain-on-scientific-publishing.github.io/website/post...

1/10 New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang's Lab! We uncover the unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs. Full story here: www.biorxiv.org/content/10.1...

Its 2025 and two atoms STILL can exist in the same space according to AF3

www.wehi.edu.au/careers/make... WEHI is looking for new lab heads! New and experienced lab heads welcome. Check out the ad, consider applying and share. We’re a collaborative bunch, in Australia, with fabulous technology, great colleagues at a values-driven organisation. @wehi-research.bsky.social

We are in the market for a benchtop FACS machine. Does anyone have recommendations for a reliable, low-maintenance instrument? We are mostly sorting mouse cells. We are currently considering the Sony SH800, Bio-Rad S3e, or similar options.

🚀 Excited to release BoltzDesign1! ✨ Now with LogMD-based trajectory visualization. 🔗 Demo: rcsb.ai/ff9c2b1ee8 Feedback & collabs welcome! 🙌 🔗: GitHub: github.com/yehlincho/Bo... 🔗: Colab: colab.research.google.com/github/yehli... @sokrypton.org @martinpacesa.bsky.social

Planning to apply for #research #funding from the ERC? From the next application rounds, expect changes to the: • proposal structure • evaluation process • extra funding you can request • eligibility for Starting & Consolidator #Grants (from 2027) More 👇 europa.eu/!RPHWvv

1 plant hormone receptor ☘️ 3,500 mutants, to single-site saturation 🧬 >45,000 binding and abundance measurements 📶 Very happy to present our latest work – where deep mutational scanning meets the world of small molecules.

 www.biorxiv.org/content/10.1...

 With @benlehner.bsky.social [1/7]