Daniel Fox

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.

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...

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

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...

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...

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.

Was an absolute pleasure to write with @cyntiat.bsky.social, Janik, @rhyswg.bsky.social and @knottrna.bsky.social 😊

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 …

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. 🤖🧪🔬

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

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

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/

🧶🧬

Thank you!!

Thank you so much for your help!!

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

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. 🩸 🦠 🔬

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

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

Many thanks to @rhyswg.bsky.social and @greening.bsky.social for supporting my application to attend! 😊

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🔬🧬

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?

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...

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...

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 ...

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...

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...

“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...

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...

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

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...

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...

Can I be added please 🙏🏼

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...

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

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!