I'm sorry all, but I am really not trying to DoS bioRxiv. I am just so excited to read all the amazing preprints you're all putting out that I am hitting those links all day [Thanks bioRxiv for running such an amazing service]

Richard Sever@richardsever.bsky.social · yesterday

bioRxiv/medRxiv have been dealing with endless bot attacks recently (plus usual DDOS stuff, etc). Tricky to address without impacting genuine users - many of you affected. Apologies. We're working with our hosting service on solutions & think we're getting there [he shouts in his Red Queen costume].

Oh my fucking god bioRxiv why

Amaze. Amaze. Amaze!

No glasses for the solar eclipse? Don’t despair. You can enjoy it with crisps on the side

Most PDB structures report one set of coordinates. But the experimental data behind them, in both X-ray crystallography and cryo-EM, is produced by an ensemble of structures. How to extract this ensemble data at scale has been a quest in structural biology for 40+ years.

Our paper on the active form of human protein kinases is out in Biochemical Journal from @biochemsoc.bsky.social . Great experience with the journal, unlike another journal that begins with "Nat" and ends with "omms." doi.org/10.1042/BCJ2... Made the cover in August (paper came out in July)...

Glad to share our new results on the interphase electric potential of biomolecular condensates.

bioRxiv Biophysics@biorxiv-biophys.bsky.social · 7d ago

Sequence-dependent molecular asymmetry and architecture define electric potential profiles of biomolecular condensates https://www.biorxiv.org/content/10.64898/2026.08.03.742525v1

Broke: Nature uses this really cool mechanism for X Woke: Look we can use this cool mechanism from nature to engineer new systems with property X Bespoke: No one knows how to do X, but our genAI figured out how to do it all by itself

Can we achieve the same scaling laws in biological AI as we have in the rest of machine learning? We found that @jura.bsky.social's mix of designed data generation and training produce robust scaling laws: more data reliably lead to better predictions over many orders of magnitude.

🧪 One small step towards a complete atlas of human sequence variant effects, a giant leap for figuring out which variants in the Autoimmune Regulator (AIRE) protein are pathogenic, and some baby steps towards understanding the AIRE protein @varianteffect.bsky.social

The American Journal of Human Genetics@ajhgnews.bsky.social · last wk.

🧬Online now! 📄Systematic and proactive evaluation of AIRE missense variant effects 🧑‍🤝‍🧑 @axakova.bsky.social @fritzroth.bsky.social & co www.cell.com/ajhg/fulltex...

Meet the inaugural winners of the Ctrl Z Award www.science.org/content/arti...

ScienceAdviser Exclusive: Meet the inaugural winners of the Ctrl Z Award

Today in Science and science: Ice age hunters’ penchant for female mammoths, a detailed vagal map, and more

science.org

We can design "static" binders routinely now, but design of "dynamic" shape-changing proteins has remained quite hard. Jeffrey Chang and I asked: why can't we couple small-molecule binding to shape change? After all, natural proteins do it every day. In a new preprint, we show how it can be done. 🧵

Why do intrinsically disordered proteins behave so weirdly during SDS-PAGE? This is the question we aim to answer in our recent paper: onlinelibrary.wiley.com/doi/10.1002/...

Sequence determinants of the hypomobility of intrinsically disordered proteins in <fc>SDS</fc>‐<fc>PAGE</fc>

Proteins with intrinsically disordered regions (IDRs) migrate at a higher apparent molecular weight in sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, complicating their analysis and...

onlinelibrary.wiley.com

Nanosecond methyl dynamics in the eukaryotic RNA exosome core https://www.biorxiv.org/content/10.64898/2026.07.25.740703v1

I guess this means I will have to give up remembering PDB IDs of key structures (1ubq, 1fmk, 1xqq, 1shf, 2ci2, 1abd, etc all played key roles in my ph.d.).

almost…

Rob Edwards@linsalrob.bsky.social · 3w ago

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

Fantastic opportunity at @pasteur.fr in Spyros’ brand new lab, especially if you like protein design 🎉

Antigen Evolution & Design Lab@antigenevo.bsky.social · 3w ago

🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st

Benchmarks of AI agentic systems remind me of bioinformatics 20 years. And not in a good way! Is anyone else getting tired of everyone reporting that they are better than everyone else according to their own new benchmark? 🤬

It’s time for the World Cup final with one of the greatest footballers that may be playing his last cup So time for a short thread on a link between Messi and an intrinsically disordered protein. 1/n

Nice moves! Haven't checked the GHR, but I got some glitter to add to the dancing queen's partner! 🍬 The hGH is glycosylated with complex sialylated (+dancing) N-glycans that regulate its serum half life; the more of those, the longer the hGH lasts 😎 (This household is going for Spain btw 😁)

It’s time for the World Cup final with one of the greatest footballers that may be playing his last cup So time for a short thread on a link between Messi and an intrinsically disordered protein. 1/n

It's nice when you benchmark your own method and find it good. But its even nicer when others benchmark your method and find it good. Figure from: Coarse-grained simulations of long intrinsically disordered proteins: a benchmark of Martini 3 force-fields doi.org/10.64898/202...

bioRxiv Biophysics@biorxiv-biophys.bsky.social · 4w ago

Coarse-grained simulations of long intrinsically disordered proteins: a benchmark of Martini 3 force-fields https://www.biorxiv.org/content/10.64898/2026.07.17.739185v1

Our new paper on SPOP, a subunit of a Cullin-RING ubiquitin ligase that is heavily mutated in cancer patients. We are describing a large-scale, quaternary structural transition that converts an autoinhibited (double donut) state into the active state! kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...

Classic Glazed Donut

ALT: Classic Glazed Donut

static.klipy.com

Join us in a fun, crazy and interesting interdisciplinary research project that combines protein biophysics, evolutionary genomics, biomolecular archaeology, and textile research to resolve species identity and post-translational modifications in the structural proteins collagen and keratin

Matthew Collins@matthewcollins.bsky.social · last mo.

Copenhagen job alert 🚨 GLOBE (@ucph.bsky.social) is hiring a 21-mo Postdoc in #Bioinformatics & #ComputationalProteomics Work with @lindorfflarsen.bsky.social, @fridowelker.bsky.social, @brandtgroup.bsky.social & more mapping collagen/keratin diversity across 1000s of genomes. 📅 Deadline Aug 31

Copenhagen job alert 🚨 GLOBE (@ucph.bsky.social) is hiring a 21-mo Postdoc in #Bioinformatics & #ComputationalProteomics Work with @lindorfflarsen.bsky.social, @fridowelker.bsky.social, @brandtgroup.bsky.social & more mapping collagen/keratin diversity across 1000s of genomes. 📅 Deadline Aug 31

Postdoc of Bioinformatics and Computational Proteomics

jobportal.ku.dk

AF-CALVADOS is now published doi.org/10.1002/pro.... We combine AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale: — Ensembles of >12000 full-length human proteins — Comparison of IDRs alone and I n context for >1500 TFs @sobuelow.bsky.social @kejohansson.bsky.social

AF-CALVADOS is now published doi.org/10.1002/pro.... We combine AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale: — Ensembles of >12000 full-length human proteins — Comparison of IDRs alone and I n context for >1500 TFs @sobuelow.bsky.social @kejohansson.bsky.social

Sometimes when I see a new ML model trained on dubious data, I’m reminded of a famous (experimental) scientist who once described a computational method as “a faster way of getting the wrong result”

Effects of residue substitutions on the cellular abundance of proteins

Effects of residue substitutions on the cellular abundance of proteins

Empirical substitution matrices from experimental measurements on 31,614 variants accurately predict cellular protein abundance changes using only amino-acid substitution and whether the site is buried...

buff.ly

In this analysis, papers that have not been posted as a preprints were retracted about twice as often as preprinted papers that were also published in a journal (19 vs 8 pr 10.000 papers). [though the authors note that there may be confounders]

Richard Sever@richardsever.bsky.social · last mo.

“move from preprint to peer-reviewed publication leaves the central claims of most abstracts intact, indicating preprints are a reliable source…papers that were never posted as preprints were retracted at roughly twice the rate of those that were…” www.biorxiv.org/content/10.6...