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Daniel Fox

@danielrfox.bsky.social
190 followers 229 following 13 posts

Postdoc in the Grinter Lab at the University of Melbourne. Interested in CryoEM, de novo protein design and host-pathogen interactions. Views my own. 🦠🔬🌈

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Reposted by Daniel Fox
Cyntia Taveneau @cyntiat.bsky.social · 18/12/2025
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
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Brett Collins @brettcollins.bsky.social · 15/12/2025
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
nature.com
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...
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Daniel Hurdiss @danielhurdiss.bsky.social · 04/12/2025
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...
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Augustinas Silale @augustsilale.bsky.social · 02/10/2025
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...
doi.org
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.
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Oli Clarke @olibclarke.bsky.social · 13/09/2025
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
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Cyntia Taveneau @cyntiat.bsky.social · 02/09/2025
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...
cell.com
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...
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Reposted by Daniel Fox
Niko McCarty @nikomccarty.bsky.social · 01/09/2025
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.
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Daniel Fox @danielrfox.bsky.social · 02/09/2025
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. 🤖🧪🔬
sciencedirect.com
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 …
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Reposted by Daniel Fox
Rhys Grinter @rhyswg.bsky.social · 25/07/2025
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
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Maciek Wiatrak @macwiatrak.bsky.social · 21/07/2025
💥 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
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Kate Michie @kmichie.bsky.social · 15/07/2025
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/ 🧶🧬
eventbrite.com
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
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Marija Dramicanin @dramarija.bsky.social · 10/07/2025
New to nature proteins are the future! Proud to have contributed to this groundbreaking work! 🏴‍☠️
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Daniel Fox @danielrfox.bsky.social · 10/07/2025
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. 🩸 🦠 🔬
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Kate Michie @kmichie.bsky.social · 02/07/2025
ASBC and Biocommons are building opportunities for researchers to discuss and explore protein design tech. First up is @rhyswg.bsky.social. Excited for this!
biocommons.org.au
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
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Daniel Fox @danielrfox.bsky.social · 03/06/2025
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🔬🧬
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David Pocock @davidpocock.bsky.social · 06/04/2025
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...
theguardian.com
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?
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Bronte Johnstone @bjohnstone.bsky.social · 30/03/2025
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.
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Luke Formosa @drlukeyform.bsky.social · 30/01/2025
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...
careers.pageuppeople.com
Job Search
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Chris Greening @greening.bsky.social · 29/01/2025
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...
nature.com
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 ...
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Marija Dramicanin @dramarija.bsky.social · 16/01/2025
“De novo designed proteins neutralize lethal snake venom toxin” paper from the Baker lab just published in Nature. www.nature.com/articles/s41...
nature.com
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...
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Jake Wintermute @synbio1.bsky.social · 15/01/2025
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...
nature.com
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...
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Cyntia Taveneau @cyntiat.bsky.social · 14/12/2024
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.com
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
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Martin Pacesa @martinpacesa.bsky.social · 08/12/2024
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...
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Cyntia Taveneau @cyntiat.bsky.social · 10/12/2024
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
biorxiv.org
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...
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bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 06/12/2024
Inhibiting heme-piracy by pathogenic Escherichia coli using de novo-designed proteins www.biorxiv.org/content/10.1101/202…
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bioRxivpreprint @biorxivpreprint.bsky.social · 06/12/2024
Inhibiting heme-piracy by pathogenic Escherichia coli using de novo-designed proteins www.biorxiv.org/content/10.1101/202…
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cryoEM papers @cryoempapers.bsky.social · 07/12/2024
Inhibiting heme-piracy by pathogenic Escherichia coli using de novo-designed proteins biorxiv.org/cgi/content/short/2024.12.05.626953v1
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Matthew Witney @virotuned.bsky.social · 09/12/2024
Nice to see this work presented recently at BDI ! Congratulations!
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Marija Dramicanin @dramarija.bsky.social · 09/12/2024
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!
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Daniel Fox @danielrfox.bsky.social · 08/12/2024
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!
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Diego del Alamo @delalamo.xyz · 27/11/2024
An RFdiffusion-generated binder conjugated to a single-chain antibody shows antitumor activity in mouse models www.biorxiv.org/content/10.1...
RF diffusion-based binder design for aiCAR-T cells targeting BCMA. a, Schematic of the RFdiffusion-based forward denoising process used to generate binders (blue) that target the extracellular domain of BCMA (gray). b, Cytotoxicity of ai- and scFv CAR-T against RPMI-8226, MM.1S, and L-363 co-cultured for 16h at various E:T ratios and normalized to the UTD control.
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Chris Lupton @luptoncj.bsky.social · 21/11/2024
Great to see our work on the #cryoem structure of the human TSC:WIPI3 lysosomal recruitment complex! Awesome effort from co-authors @charlesbj.bsky.social and Laura D'Andrea with @drellisdon.bsky.social doing the heavy lifting leading the project. www.science.org/doi/10.1126/...
science.org
Structure of the human TSC:WIPI3 lysosomal recruitment complex
The complete TSC structure reveals how lysosomal targeting proteins and phosphoinositides coordinate mTORC1 inhibition.
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Andrew Ellisdon @drellisdon.bsky.social · 20/11/2024
Our latest study is now online at Science Advances! We report the structure of the gigantic TSC:WIPI3 complex revealing new insights into lysosomal docking and dysregulation in disease. #cryoEM #mTOR 🧪 www.science.org/doi/10.1126/...
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Charles Bayly-Jones @charlesbj.bsky.social · 20/11/2024
🚨 Our story on the TSC:WIPI3 lysosomal-recruitment complex is now live in Science Advances. Equal-first co-authors @luptoncj.bsky.social & Laura D'Andrea. Work lead by @drellisdon.bsky.social. Funding from @deptofdefense.bsky.social & Australian Research Council. www.science.org/doi/10.1126/...
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Charles Bayly-Jones @charlesbj.bsky.social · 14/11/2024
Another really nice highlight of our recent work. Arun et al raise interesting points about membrane cross talk and next-steps for LYCHOS. www.cell.com/cell/abstrac...
cell.com
Bound by the love for cholesterol: A transporter meets a GPCR
In a recent issue of Nature, Bayly-Jones et al. report the cryo-EM structures of a lysosomal cholesterol sensor, LYCHOS, also known as GPR155, which reveals a unique fusion of a plant auxin-transporte...
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Chris Lupton @luptoncj.bsky.social · 14/11/2024
Very cool to see our work on the #cryoEM structure of LYCHOS as the Editor's Choice in Science Signalling! Thanks @jffoley.bsky.social !!
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Matthew Witney @virotuned.bsky.social · 19/11/2024
Finally out! Our contribution to a better understanding of quantitative features of virus p:MHC epitopes. We compared 45 vaccinia epitopes and their source antigens across multiple cell lines, over time, and from the spleen on infected mice against T cell responses in mice.
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