Excited to present sampleworks: a modular platform for generating biomolecular conformational ensembles by coupling AI structure predictors to experimental data. Our first publication of @diffuseproject.bsky.social, led by @karsonchrispens.bsky.social + Marcus Collins. thestacks.org/publications...

Aggregating many experiments into one zero-shot protein language model score obscures that current models cannot meaningfully rank a set of fit mutations or prioritize new-to-nature functions @clauswilke.com www.biorxiv.org/content/10.6...

We just preprinted DropSynth-Gold where we replaced PCA with Golden Gate Assembly (GGA) inside emulsion droplets, extending multiplexed gene synthesis to ~3 kb constructs assembled from up to 12 fragments while preserving the scalability of DropSynth. 1/n

I will probably be hiring either a PhD or a Postdoc in the near future. If you are interested in deep biochemical history or molecular mechanisms of evolution please get in touch.

We are recruiting! If you are passionate about technology development, protein engineering, computational design, directed evolution, chemical biology - please reach out! (The setting is pretty nice too…)

Excited to share Sampleworks led by @karsonchrispens.bsky.social with @diffuseproject.bsky.social. It's a modular framework connecting structure predictors to experimental data and guidance methods. Swap predictors or guidance methods. All open and made to be built upon. t.co/fvNHH3gfVu

Radial is live! A new organization at @asterainstitute.bsky.social bringing together structural biologists, engineers, and ML scientists to redesign how we do science. @statnews.com has the story: www.statnews.com/2026/03/11/r...

We made FLIP2, a protein fitness benchmark spanning seven new datasets, including enzymes, protein-protein interactions, and light-sensitive proteins, as well as splits that measure generalization relevant to real-world protein engineering campaigns.

This is why I can’t stand LinkedIn.

Crystal structure of malaria parasite fusogen PfHAP2 domain 3 and nanobodies - unsolved mysteries galore! 🦟🦙💎 PfHAP2 is part of family of ancient fusogens involved in fertilisation processes in algae, plants to malaria parasites. Check out the first crystal structure of PfHAP2 D3 and nanobodies

Beginning 2026 with a flipping good paper🚀 OSCA/TMEM63 proteins do double duty: they’re ion channels and mechanically activated lipid scramblases helping reshape membranes and survive mechanical stress. 👏 @yiechanglin.bsky.social @charlesdcox.bsky.social doi.org/10.1038/s414...

Pfs48/45 nanobodies block malaria parasite transmission 🦟 and crystal structures provide structural insight to how they bind 💎 Pfs48/45 is one of the leading transmission blocking vaccine candidates and a critical fertilisation antigen 💕 Please share widely- love to hear your feedback!

🧵1/3 I created this free 37-hour course, distributed across 10 lectures, to introduce AI-based protein design. For more information about the course and its specific topics, please visit the official course page:

New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! www.biorxiv.org/content/10.6...

www.biorxiv.org/content/10.6... most proteins are multi domain but our understanding of how architectures evolve is limited - we mapped 40K chitinases and show a stepwise “grammar” of domain gain/loss and localisation changes that predicts ecological strategy and physiological function.

I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests. Thread below - but first some links: A longer take: fraserlab.com/2025/12/29/k... Preprint: www.biorxiv.org/content/10.6...

Keen to use an open source workflow for nanobody discovery? Check out Alpseq 🦙 Alpseq’s diversity analysis, enrichment counts & clustering allow different approaches for nanobody selection Great collab with bioinformaticians @qgouil.bsky.social Kathleen Zeglinski www.biorxiv.org/content/10.1...

Pigeon fortress

Pomfret Vermont 📸 Ngoc Minh

H.M. Saffer II (American, b.1942) : Moon Waters, 2023 Oil on canvas 30 × 30 in | 76.2 × 76.2 cm Further description & bio in the alt text 👇

‘Protein evolution as a complex system’ – A new Comment discusses protein evolution in terms of complex systems theory and machine learning approaches to model the dynamics of protein evolution www.nature.com/articles/s41...

Thank you everyone for the congratulations and the large number of applications! I want to specifically encourage applications for these positions: * Postdoc in structural biology (cryoEM, ideally with X-ray too) * Full time lab manager/technician with wetlab experience

Protein-ligand complexes are all the rage with OpenBind+other efforts launching 3 amazing papers describing 229 protein-ligand structures just dropped in @actacrystd.iucr.org A tremendous teaching text, but I disagree on the discussed potential for misuse. Read more fraserlab.com/2025/07/29/E...

Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!

Pleased to announce I have been promoted to the rank of GRANDMASTER thank you for your attention to this matter

Proud to share our work where we resolved a longstanding question regarding the existence of a human telomerase dimer and provided insights into its function. Led by 3 amazing lab members in collaboration with @yiliangding.bsky.social and @rdaslab.bsky.social. www.science.org/doi/10.1126/...

This paper started probably 20 years ago when I was working with John Oakeshott, a long time in the making and I think a nice summary of a complex real world evolutionary process

Seriously. Pay for review, not publication Publish public reviews Editorial assessment changes until version of record Flexible article types elife-rp.msubmit.net/html/elife-r... Some work todo on reviewer credit (add @prereview.bsky.social to you cv!)

New tools! GreenPy and ApplePy are fluorescent biosensors for pyruvate with huge responses (20–40x in vitro) and a range of affinities (10s of μM to mM). These should be game changers for imaging of metabolism! Great work by Shosei Imai @sikmys.bsky.social and team 👏. www.biorxiv.org/content/10.1...

Average zero-shot mutation effect predictions across related sequences to reduce noise and improve accuracy. @cwjpugh.bsky.social @paulinanunezv.bsky.social @jonnyfrazer.bsky.social Mafalda Dias www.biorxiv.org/content/10.1...

Canberra has excellent sky

We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org. A great position for someone who is looking to be a tech for a few years before grad or med school. aprecruit.ucsf.edu/JPF05424

🚨 preprint 2️⃣ this month: our (purely experimental🧪) venture into #ChemBio We prouldy present: ADD-tagging of proteins (or "ADDing") —a super convenient enzymatic technique to install click chemistry handles on proteins. Led by superstar @wahyuwidodo.bsky.social www.biorxiv.org/content/10.1... A 🧵👇🏽

Are you (or a recent grad or tech/lab manager) looking for an awesome, mission-driven job? Come join us @addgene.bsky.social! Put your lab skills to work making impact for thousands of scientists around the world 💪🧬🧪

Protein Engineering, Design & Selection (PEDS) invites contributions to a Special Collection titled, “Non-Canonical Amino Acids", with guest editors Prof. Huiwang Ai (Virginia) and Prof. Peng Chen (Peking). Send us your best work! academic.oup.com/peds/pages/c...

Some interesting links I'm collecting for folks who want to do advocacy in their local districts. www.ucsf.edu/cgr/advocacy... - easy way to write to your reps! sciencehomecoming.com - write a letter to a hometown newspaper (great for where you grew up or went to undergrad/grad school)

Good autumn in Canberra

Choosing ML architectures for protein engineering is often challenging. Our “new” updated preprint provides a rational framework to match ML models to protein fitness tasks, showing landscape ruggedness influences prediction accuracy. Mahakaran dana Adam et al www.biorxiv.org/content/10.1...

Fractal cabbage

Good read: Inside arXiv - the Most Transformative Platform in All of Science www.wired.com/story/inside...

www.biorxiv.org/content/10.1... why are protein fitness landscapes often very rugged and what does this mean for evolution and engineering? We have been interested in this for a while - in this paper (led by Matt Spence) we look at it quantitatively using eg spectral graph theory.

We unlock breakthrough insights by delivering the best training sets in biology—at unprecedented scale. youtu.be/KuCaJTPHM2o

biorxiv.org/content/10.1... Here’s a paper that was many years in the making. The idea that the climate can affect the thermodynamic mechanism of binding due to the temperature dependence of the entropy term is interesting- we see gradual shift in binding mode along evo trajectory…

Our review on machine learning methods to study sequence–ensemble–function relationships in disordered proteins is now out in COSB authors.elsevier.com/sd/article/S... Led by @sobuelow.bsky.social and Giulio Tesei

‘Travel agencies charge far more than it would cost an academic to arrange their own travel and accommodations - sometimes staggeringly more.’

Isolated in just 3 years! (previously, 12 years). We obtained two strains from 'Hodarchaeales', proposed to be closest to our archaeal ancestor. Our analysis suggests the ancestor was an anaerobic, syntrophic, peptidotrophic, archaeon with a simple intracellular structure and possible aerotolerance.