Fall is beautiful, even on gray days 🍂 🍁

Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).

My 11yo is more active in her Teams chats than I am in mine.

Danish design cup

Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...

The UNC Department of Biology is seeking a Director of Biology Teaching Labs, a key leadership role overseeing our undergraduate laboratory program. 1/n Learn more and apply here: unc.peopleadmin.com/postings/308...

I have a very bad feeling about this...

Alternatively, lads, might be worth thinking about supporting the German car industry to remain viable in the future rather than locking them into a dying business model. But sure, you go off...

Airplane sunrise is the reward for early departures. Looking forward to European RosettaCon 2025!

Kiel

Ah, a classic moment of @nature.com recognizing the scientific contributions of both genders: man and machine.

You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly. This saves some clicking around. Neat!

As I tell my students, if you arrived at a simple answer in biology you have done one of two things: arrived at the wrong answer or asked the wrong question

Kindergarten teacher asks what I teach (biological sequence analyses), I try to explain. She turns to the 3yo and asks „What do you want to be when you grow up?“ Prompt and confident answer: „A butterfly 🦋!“

The proteasome-substrate-shuttle protein UBQLN2 contains—like other quality control system proteins—a long region devoid of lysine (a lysine desert) Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation doi.org/10.1101/2025...

For every Nobel that goes to a criminally under-recognized woman scientist (Brunkow, Karikó), or fails to go (Candy Lee), a week of mourning and reform for an academic system wherein you can do Nobel-prize-worthy-work and still end up without a conceivable path to being a professor.

Fun & action the local science museum #experimentarium

This October I’m drawing one molecule a day inspired by proteins in pdb @rcsbpdb.bsky.social Day 2/31 Prompt WEAVE N-terminal domain of a Fibrion - a building block of silk fiber produced by silkworms. Pdb: 3UA0 Next prompt is CROWN and I would love your suggestions!

Some interesting thoughts on the Perspective Harper Raiken and I wrote over the summer

I don’t know who wrote this, but it’s absolutely perfect

Why are transcription factors disordered? Come join us in Oxford as a postdoc and we'll find out together! Help publish 3 mature projects, AND develop cool new single molecule fluorescence binding assays! biophysics transcription protein:DNA interactions my.corehr.com/pls/uoxrecru...

Recruiting the next generation of bioinformatics students

We’re recruiting a PhD Fellow in Computational Systems Immunology. Work on large-scale immune receptor datasets and develop computational models in close collaboration with experimental labs. Apply here: www.jobbnorge.no/en/available...

Interesting episode of short wave about the origin of endometriosis. I really appreciate that they end with how uncertainty in NIH funding affects the future of their work. www.npr.org/2025/09/26/n...

The EMBL PhD programme is open until 13th October (entry ~Sep 2026): www.embl.org/about/info/e... We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

Job opportunities at an absolutely amazing place for molecular biology 🧫

Almost done, just need to add a bit of background.

Different supervision task today 🍿

Deadline extended - last chance, second edition!

Cool project with the Pless lab on disease-associated variants in a membrane protein, NALCN, that needs to be in complex to function. Most of our computational work was done by PhD student Aleks Panfilova.

Interested in structural biology, membrane proteins, biophysics and working to understand hormone transport in plants?☘️🔬👩‍🔬🧪 We have an open PhD position: - 3 years fully funded. - Details and application link: www.linkedin.com/posts/plant-... Please repost 💚

The journal version of "Biophysics-based protein language models for protein engineering" with @philromero.bsky.social is live! Mutational Effect Transfer Learning (METL) is a protein language model trained on biophysical simulations that we use for protein engineering. 1/ doi.org/10.1038/s415...

🎯

🚨 We're hiring, please share! The FMI seeks a tenure-track Group Leader (Assistant Prof) in Structural Biology 🔬 Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...

One of those days when Copenhagen is trying to play San Francisco 🌫️ Fortunately we got to keep the trains.

"We can and should reject that AI output is ‘good enough,’ not only because it is not good, but also because there is inherent value in thinking for ourselves."

BIG NEWS!! We will be hiring a new professor with 25 years of endowed funding at the @biozentrum.unibas.ch @unibas.ch, focused on using biophysics and structural biology to explore climate-related fundamental science topics. Come start an innovative research cluster with us! 🧪🔬🧶🧬🌾🌍

Successfully taught my first bioinformatics class in Danish 🇩🇰 Based on feedback, the most helpful bit was rather language-Independent, when I said that affine gap scores are kinda like Affinity in Magic The Gathering 🧙‍♀️ 📜

A very relatable rant on why manuscript revisions can be frustrating. And it doesn’t even mention „you should have cited these 7 tangentially related articles, all written by the same author“ 📜

This is where German clearly was much easier. To this day I can find myself in an English audiobook and realise „oh that’s how you pronounce it“ 😅

Final reminder to nominate yourself / your outstanding group members for the inaugural ISBUC Best Paper Award 📅 Submission deadline: September 3rd 🏆 Prize: 10.000kr stipend for research and training-related travel expenses ✏️ Submit nominees: isbuc.ku.dk/junior-isbuc...

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

#lørdagslik (Saturday sweets) from Frauke Gräter at the SBiNLab 25th anniversary symposium: Natural proteins are like soft candy (gummy bears) while current designed proteins are like hard candy 🍭

starting to suspect my neighbor is a large language model

Last chance to register for the 2025 European RosettaCon - we had a blast last year, and @ajasjaljubetic.bsky.social is putting together a great program. With Easter eggs 🥚 in the submission system!

If you use Boltz1/2, BioEmu, Chai1, or other MSA-dependent models, you’re likely using our ColabFold server. Please be considerate! Avoid large submissions across many IPs instead generate the MSA locally. Our server is an old-timer from 2014 and can’t handle that load.

RosettaFold 3 is here! 🧬🚀 AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release! Congratulations @simonmathis.bsky.social and team!!! ❤️ bioRxiv preprint: www.biorxiv.org/content/10.1...

I'm in this picture and I don't like it

Testing how AI-proof my homework and exam questions are. Images and graphs are a real challenge for current LLMs. This "HMM" for membrane proteins look nothing like the real deal.

Instead of regurgitating the bromide that LLMs are just "autocomplete on steroids" (even by people who know better), maybe we can actually engage in some public education. The problem with genAI is better expressed through a classic computer science concept, known as SYMBOL GROUNDING. 🧵