Big milestone for the AI Protein Design Program last November: our first AI binder design workshop! Proud of the team and grateful to @kmichie.bsky.social for her amazing talk. This is just the beginning… excited for what’s next! #AI #ProteinDesign #AIPDP

Congratulations to the Landsberg lab for a fantastic paper in Nat Comms on the structure of the YenTC toxin. Led by Yu Shang Low and Solace Roche. @dr-berger.bsky.social @sarahjpiper.bsky.social

Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins - Nature Communications

ABC toxins are bacterial insecticides with biotechnological potential. Here, Low et al. have deciphered soluble and membrane-inserted structures of YenTc that highlight structural and mechanistic dive...

nature.com

How can AI and #cryoEM help save some of the biggest babies on the planet? 🐘🔬 Our new preprint identifies Elephant Herpesvirus gH/gL/gO as a receptor-binding complex and a promising vaccine candidate, now being tested in young elephants across European zoos! 💉 www.biorxiv.org/content/10.6...

Our paper on the Bacteroidota BAM complex is out in @natmicrobiol.nature.com! With @madejmar.bsky.social We found that BAM in Bacteroides and Porphyromonas gingivalis has a distinct architecture from BAM in Proteobacteria. doi.org/10.1038/s415...

Structure of a distinct β-barrel assembly machinery complex in the Bacteroidota - Nature Microbiology

Structural and functional characterization of the β-barrel assembly machinery complex in Bacteroidota reveals a distinct, seven-component complex with a large extracellular domain that may enable β-barrel–surface lipoprotein complex assembly.

doi.org

This one is a bit of a departure from the usual and definitely a work in progress! We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below. Read on for details... 1/x

bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles https://www.biorxiv.org/content/10.1101/2025.09.08.674935v1

Excited to share our new review on AI-driven protein design - from its origins to today’s breakthroughs, methods, potential, and challenges ahead ! www.cell.com/structure/fu...

Code to complex: AI-driven de novo binder design

In this review, Fox et al. discuss how artificial intelligence has transformed our ability to design new-to-nature proteins that bind target proteins with high affinity and specificity. The authors de...

cell.com

Out today: A useful review on AI-designed protein binders. It covers the history of this work + has lots of good case studies, including how these tools are being used to make snake anti-venoms. The tables are particularly valuable.

Quite proud of this one. Our review on AI-designed de novo binders out now in Structure. We give a brief history, outline the current ecosystem, highlight some standout applications and discuss the need for regulatory discussions. 🤖🧪🔬

Code to complex: AI-driven de novo binder design

The application of artificial intelligence to structural biology has transformed protein design from a conceptual challenge into a practical approach …

sciencedirect.com

Did you know that some bacteria can generate ATP, the energy currency of life, literally out of thin air? 🌬⚡️ In PNAS today, we show how bacteria can do this using just three enzymes. Honoured to contribute to this study with Christoph von Ballmoos, Chris Greening and Gregory Cook lnkd.in/gxm8SXxF

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve. Preprint 📝: biorxiv.org/content/10.1... 🧵 1/n

Last reminder- Dr Rhys Grinter webinar @rhyswg.bsky.social is on in just a couple of hours- click through to obtain the link. #proteindesign #structbiol You can sign up for future event information and reminders here: australian-structural-biology-computing.github.io/website/ 🧶🧬

WEBINAR: Leveraging deep learning to design custom protein-binding proteins

Be inspired by case studies that show you how deep learning methods are speeding up the process of designing custom proteins

eventbrite.com

New to nature proteins are the future! Proud to have contributed to this groundbreaking work! 🏴‍☠️

Rhys Grinter@rhyswg.bsky.social · last yr.

Excited to share our latest work using AI-designed proteins to block heme-piracy by E. coli. Published in @natcomms.nature.com. A team effort between my lab and the ‪‪@knottrna.bsky.social‬ ‬lab, with experimental work led by the talented @danielrfox.bsky.social www.nature.com/articles/s41...

Proud to share some of the work from my PhD is now out in Nature Communications! Very grateful to all coauthors who helped make this happen, especially my supervisors @rhyswg.bsky.social and @knottrna.bsky.social for their support. 🩸 🦠 🔬

Rhys Grinter@rhyswg.bsky.social · last yr.

Excited to share our latest work using AI-designed proteins to block heme-piracy by E. coli. Published in @natcomms.nature.com. A team effort between my lab and the ‪‪@knottrna.bsky.social‬ ‬lab, with experimental work led by the talented @danielrfox.bsky.social www.nature.com/articles/s41...

ASBC and Biocommons are building opportunities for researchers to discuss and explore protein design tech. First up is @rhyswg.bsky.social. Excited for this!

WEBINAR SERIES: Leveraging deep learning to design custom protein-binding proteins — Australian BioCommons

Be inspired by case studies that show you how deep learning methods are speeding up the process of designing proteins with desirable biophysical properties. More information Register

biocommons.org.au

Grateful to have been awarded an ASBMB Fellowship and a YSP Fellowship to be able to present my work at the Young Scientist Program and at the FAOBMB2025 Conference. It was a great opportunity to network with other students and ECRs and was completely inspired by all the cool science🔬🧬

96% of Australians want more done to protect nature. Meanwhile, just 0.06% of the budget went to on-ground biodiversity programs. We’re losing species we love & major parties are sleepwalking through it. Australians care. It’s time politicians did too. www.theguardian.com/australia-ne...

Australia is in an extinction crisis – why isn’t it an issue at this election?

Some of the country’s most loved native species, including the koala and the hairy-nosed wombat, are on the brink. Is this their last chance at survival?

theguardian.com

Excited to share that our work on a family of pore-forming proteins is now live in Science Advances! We show structural snapshots across the entire pore-forming pathway for a cholesterol-dependent cytolysin-like (CDCL) bicomponent system.

We are hiring! The Formosa Group is hiring a Research Officer to join our program on #Mitochondria, #Metabolism & #MitochondrialDisease at the Monash BDI! 💡If you're passionate about mitochondrial research or know someone who is, please share! Apply now: careers.pageuppeople.com/513/cw/en/jo...

In Nature Chemical Biology today, we reveal how microbes clean our atmospheres by consuming carbon monoxide (CO) gas. A methodological tour de force from Ashleigh Kropp, Rhys Grinter, and David Gillett with broad implications for the atmosphere and bioenergetics. www.nature.com/articles/s41...

Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria - Nature Chemical Biology

Here, Kropp et al. use cryo-electron microscopy and structural modeling to show that the enzyme [MoCu]-CO dehydrogenase interacts with its partner, the membrane-bound quinone-binding protein CoxG, to ...

nature.com

“De novo designed proteins neutralize lethal snake venom toxin” paper from the Baker lab just published in Nature. www.nature.com/articles/s41...

De novo designed proteins neutralize lethal snake venom toxins - Nature

Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...

nature.com

This pretty much settles it: we're entering the era of low-cost, on-demand binders for everything Excited to see what people build now that "inject a llama with some junk and bleed it a month later" is no longer the cutting-edge tech www.nature.com/articles/s41...

De novo designed proteins neutralize lethal snake venom toxins - Nature

Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...

nature.com

This is such a cool initiative! DL4Proteins is democratizing deep learning for protein design and prediction at a pivotal time in science—a fantastic step toward making advanced protein engineering accessible to all! github.com/Graylab/DL4P...

GitHub - Graylab/DL4Proteins-notebooks: Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

Colab Notebooks covering deep learning tools for biomolecular structure prediction and design - Graylab/DL4Proteins-notebooks

github.com

We updated our BindCraft preprint with lots of new exciting results! We release all our binder sequences and models, include more in silico analysis, novel design targets, and present AAV retargeting to specific cell types using de novo binders! www.biorxiv.org/content/10.1...

Excited to share my first-author preprint from the Knott Lab! Using de novo protein design, we developed anti-CRISPRs to potently inhibit CRISPR-Cas13. Thanks to my amazing co-authors ! www.biorxiv.org/content/10.1... #CRISPR

De novo design of potent CRISPR-Cas13 inhibitors

CRISPR-Cas systems are transformative tools for gene editing which can be tuned or controlled by anti-CRISPRs (Acrs) - phage derived inhibitors that regulate CRISPR-Cas activity. However, Acrs that ar...

biorxiv.org

Inhibiting heme-piracy by pathogenic Escherichia coli using de novo-designed proteins https://www.biorxiv.org/content/10.1101/2024.12.05.626953v1

Inhibiting heme-piracy by pathogenic Escherichia coli using de novo-designed proteins https://www.biorxiv.org/content/10.1101/2024.12.05.626953v1

Inhibiting heme-piracy by pathogenic Escherichia coli using de novo-designed proteins biorxiv.org/cgi/content/short/2024.12.05.626953v1

Nice to see this work presented recently at BDI ! Congratulations!

Daniel Fox@danielrfox.bsky.social · 2y ago

The first major body of work from my PhD is now up on BioRxiv! We used AI-designed binders to block the uptake of heme from hemoglobin through ChuA, a heme transporter found in pathogenic E. coli. 🦠🩸🔬 I’m very grateful for my supervisors and all coauthors for their support!

Australia's got de novo binders! 🎉 Congrats to @danielrfox.bsky.social @rhyswg.bsky.social, @cyntiat.bsky.social, @gavinjknott and all authors on their incredible work featured in two preprints below. Thrilled to have contributed to the ChuA story, such an exciting advance in Protein Biochem!

Rhys Grinter@rhyswg.bsky.social · 2y ago

Excited to share our first foray in ML-guided protein design. With the @gavinjknott lab we designed protein binders as that block heme piracy by pathogenic E. coli and potently inhibit CRISPR-Cas13. www.biorxiv.org/content/10.1..., www.biorxiv.org/content/10.1...

The first major body of work from my PhD is now up on BioRxiv! We used AI-designed binders to block the uptake of heme from hemoglobin through ChuA, a heme transporter found in pathogenic E. coli. 🦠🩸🔬 I’m very grateful for my supervisors and all coauthors for their support!

Rhys Grinter@rhyswg.bsky.social · 2y ago

Excited to share our first foray in ML-guided protein design. With the @gavinjknott lab we designed protein binders as that block heme piracy by pathogenic E. coli and potently inhibit CRISPR-Cas13. www.biorxiv.org/content/10.1..., www.biorxiv.org/content/10.1...