TTPD Episode 9 with @fraserlab.com: I Can Do It With a Broken Grant Cycle (Sorry for the crappy audio in places!) Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools wankowiczlab.com/2025/11/24/T...

Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.

One of these is Figure 1 from my first paper and the other is an image generated using Nano Banana Pro solely from the caption of Figure 1 of my first paper

Italian researchers (and Batman) conducted a field study on the Milan metro (138 rides)... ⬇️ "Passengers were significantly more likely to offer their seat when Batman was present (67.21% vs. 37.66%, OR = 3.393, p < 0.001)" I can smell IgNobel pmc.ncbi.nlm.nih.gov/articles/PMC...

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

Jeg står her omkring i morgen fra ca. kl 10 og frem til 11:30 eller der omkring. Så går turen videre til Panum. Håber vi ses!

Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1

Since you ask. From the birth of quantum to the birth of CERN.

My first full contribution from my time in @opig.stats.ox.ac.uk is now out! Together with @fspoendlin.bsky.social (and with contributions from King Ifashe), we created FlAbDab and FTCRDab: two large-scale, open molecular dynamics datasets to study flexibility in immune receptors.

😱 I worry the next step is to allow spaces in filenames

Uncovering the flexibility of CDR loops in antibodies and TCRs through large-scale molecular dynamics https://www.biorxiv.org/content/10.1101/2025.11.10.687725v1

Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...

🎙️ Next up Dec 2 in VESS! Thea Schulze (Lindorff-Larsen Lab): Predicting mutated protein abundance @tkschulze.bsky.social Taylor Mighell (Lehner Lab): Massive mutagenesis to understand GPCRs @taylor-mighell.bsky.social 🔗 More info at varianteffect.org/seminar-series @varianteffect.bsky.social

*If you would like to be considered for a talk at this workshop, please register & submit an abstract by 7 November* We also have a fantastic line-up of invited speakers: Matteo Degiacomi, Lucie Delemotte, Weria Pezeshkian, Mohsen Sadeghi & Ilpo Vattulainen Registration: aias.au.dk/events/show/...

Probing the energy landscape of α-Synuclein amyloid fibril formation by systematic K-to-Q mutagenesis https://www.biorxiv.org/content/10.1101/2025.11.01.685997v1

Anyway, we need some joy, so here's the Egyptian foreign minister being given a Lego Pyramid by the Danish foreign minister.

I’m excited to be speaking at the AI in Science Summit 2025 in my home town of Copenhagen #AIS25 #AI4Science I will be speaking about how AI and biophysics can come together to study protein dynamics

🔬 CECAM Workshop: “Integrative and Multiscale Modelling Approaches to Illuminate CryoEM/ET Data” Join us in Toulouse, 24–26 March 2026, to explore how molecular simulations, AI tools, can be integrated to cryo-EM and cryo-ET data. 🧬 Selection: brief CV + motivation letter required. Apply 👇

Quantum computers - what are they and how will they change things? Have a listen/watch here: @timcoulson.bsky.social and I chat with Ian Walmsley, newly appointed director of the Oxford Quantum Institute: The Science and Promise of Quantum Computing youtu.be/sPTyvBKJruU

Where Parisians post their preprints…

Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods doi.org/10.1093/bioi...

Not just #YAAFC

I attended a summer school on Spetses 🇬🇷 just as I was beginning my PhD. Looks like I will be going again in 2026 with "Lost in Integration vol. 2". Details to follow.

New review on experimental datasets that can be used to benchmark protein force fields. And if that doesn’t tickle your fancy, the data can also be used to benchmark machine learning models for biomolecular structure and dynamics.

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...

📜 New preprint! We developed PoGö, an algorithm to optimize the essential dynamics of GöMartini proteins based on all-atom simulations: www.biorxiv.org/content/10.1...

Just because this came up a few times recently If you need to compare two or more ensembles (like RMSD for structures) we developed algorithms and code (ENCORE) to do just that Similarity Measures for Protein Ensembles journals.plos.org/plosone/arti... ENCORE journals.plos.org/ploscompbiol...

Looking forward to hosting Kresten Lindorff-Larsen's talk tomorrow. I am looking forward to seeing ISTA's main lecture hall of full, and hearing the latest developments of tools to predict, design and study intrinsically disordered proteins. @istaresearch.bsky.social

Looking forward to visit colleagues in Vienna and Graz 🇦🇹 If you’re in Vienna I’m speaking on: Prediction and Design of Intrinsically Disordered Proteins and Condensates (27/10 ISTA) & Understanding the Effects of Missense Variants Using Analyses of Protein Stability and Conservation (30/10 VBC)

Remember, everyone, the best publication metric is the one that makes *your* publication record look the best.

A machine learning method for calculating highly localized protein stabilities https://www.biorxiv.org/content/10.1101/2025.10.21.683809v1

**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: [email protected]

We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale See preprint for: — Ensembles of >12000 full-length human proteins — Analysis of IDRs in >1500 TFs 📜 doi.org/10.1101/2025... 💾 github.com/KULL-Centre/...

We're excited to present LeaVS, a method to scale up learning for protein function models. It is based on the co-design of wet lab experiments and in silico training.

Submit your BPS T&C subgroup nominations::!!

We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale See preprint for: — Ensembles of >12000 full-length human proteins — Analysis of IDRs in >1500 TFs 📜 doi.org/10.1101/2025... 💾 github.com/KULL-Centre/...

I’ve met a few on the “right” path

We thank reviewer 2 for their constructive suggestions and have updated our manuscript accordingly

I wrote a blog post about the future of structural bioinformatics. Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs? Let me know what you think. jgreener64.github.io/posts/struct...

Registration now open for the '3rd Annual Danish Workshop on Advanced Molecular Simulation' Join us in beautiful Aarhus for a 2-day workshop on biomolecular simulations! 9-10 December 2025 Link for registration: aias.au.dk/events/show/...

Remember this paper "Low overlap of transcription factor DNA binding and regulatory targets" ? (www.nature.com/articles/s41...) well, well, well 🍿 ⬇️ www.biorxiv.org/content/10.1...

Dynamical buffering of reconfiguration dynamics in intrinsically disordered proteins https://www.biorxiv.org/content/10.1101/2025.10.12.681911v1

new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...

📣 One week left to register for general participation and submit poster registrations for the ISBUC Annual Meeting 🗣️Confirmed speakers for 2025 include: Tom Muir, Doryen Bubeck, Holger Stark, Simon Scheuring 📄Click here for the program and to register: bit.ly/3IonBtH

Looking forward to visit @friedlab.bsky.social @jhu.edu on Tuesday Oct 14th to talk about Prediction and Design of Intrinsically Disordered Proteins and Condensates 🍝💦 chemistry.jhu.edu/event/the-ep...

Our work developing a maximum entropy reweighting method to refine all-atom ensembles of IDPs with extensive NMR and SAXS datasets is now out in @natcomms.nature.com: rdcu.be/eKlK7 Led by @dartmouthchem.bsky.social graduate student Kaushilk Borthakur in collaboration with @bonomimax.bsky.social

This October I’m drawing one molecule a day inspired by proteins @rcsb.bsky.social Day 1/31 Prompt MUSTACHE Pdb 2QZI Let’s start with something fun: Mr. Potato head’s ‘stache is made of Androgen Receptor that binds testosterone and helps maintain his male phenotype Next prompt: WEAVE suggestions?

My HPLC was definitely overlooked www.nature.com/articles/d41...

I found out that Neurosnap offers ESMFold via API neurosnap.ai/service/ESMF... I may test how many calls are possible with the free academic plan to see if it is worthwhile to update my repo.

Spread the word if you can. We have an unused stopped flow accessory from Applied Photophysics. We traded in our Chirascan CD instrument so we have no use for this anymore. Reach out if you are interested and can find a home for this setup. Will ofcourse only work with a Chirascan!