Lightnews — Scholar-powered news

Reposted by Daniel Fox

Augustinas Silale @augustsilale.bsky.social · 7d

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

4 21 50

Reposted by Daniel Fox

Oli Clarke @olibclarke.bsky.social · 27d

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

18 81 260

Reposted by Daniel Fox

Cyntia Taveneau @cyntiat.bsky.social · Sep 2

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...

www.cell.com

1 6 20

Reposted by Daniel Fox

Niko McCarty @nikomccarty.bsky.social · Sep 1

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.

1 3 11

Daniel Fox @danielrfox.bsky.social · Sep 2

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

1

Daniel Fox @danielrfox.bsky.social · Sep 2

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 …

www.sciencedirect.com

1 5 19

Reposted by Daniel Fox

Rhys Grinter @rhyswg.bsky.social · Jul 25

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

This link will take you to a page that’s not on LinkedIn

lnkd.in

1 6

Reposted by Daniel Fox

Maciek Wiatrak @macwiatrak.bsky.social · Jul 21

💥 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

3 59 91

Reposted by Daniel Fox

Kate Michie @kmichie.bsky.social · Jul 14

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

www.eventbrite.com

1 5 6

Daniel Fox @danielrfox.bsky.social · Jul 10

Thank you!!

Daniel Fox @danielrfox.bsky.social · Jul 10

Thank you so much for your help!!

1

Reposted by Daniel Fox

Marija Dramicanin @dramarija.bsky.social · Jul 10

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

Rhys Grinter @rhyswg.bsky.social · Jul 9

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...

Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins - Nature Communications

Many pathogens encode transporters that extract heme directly from host proteins. In this study, the authors demonstrate the utility of de novo-designed proteins in understanding the mechanism behind ...

www.nature.com

1 3

Daniel Fox @danielrfox.bsky.social · Jul 10

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 · Jul 9

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...

Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins - Nature Communications

Many pathogens encode transporters that extract heme directly from host proteins. In this study, the authors demonstrate the utility of de novo-designed proteins in understanding the mechanism behind ...

www.nature.com

2 3 16

Reposted by Daniel Fox

Kate Michie @kmichie.bsky.social · Jul 2

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

www.biocommons.org.au

4 8

Daniel Fox @danielrfox.bsky.social · Jun 2

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

1 2

Daniel Fox @danielrfox.bsky.social · Jun 2

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🔬🧬

1 1 4

Reposted by Daniel Fox

David Pocock @davidpocock.bsky.social · Apr 6

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?

www.theguardian.com

9 100 290

Reposted by Daniel Fox

Bronte Johnstone @bjohnstone.bsky.social · Mar 30

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.

3 9 32

Reposted by Daniel Fox

Luke Formosa @drlukeyform.bsky.social · Jan 30

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...

Job Search

careers.pageuppeople.com

4 5

Reposted by Daniel Fox

Chris Greening @greening.bsky.social · Jan 29

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 ...

www.nature.com

33 72

Reposted by Daniel Fox

Marija Dramicanin @dramarija.bsky.social · Jan 16

“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...

www.nature.com

1 4 13

Reposted by Daniel Fox

Jake Wintermute @synbio1.bsky.social · Jan 15

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...

www.nature.com

3 18 72

Reposted by Daniel Fox

Cyntia Taveneau @cyntiat.bsky.social · Dec 14

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

1 3 10

Reposted by Daniel Fox

Martin Pacesa @martinpacesa.bsky.social · Dec 8

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...

1 31 130

Daniel Fox @danielrfox.bsky.social · Dec 11

Can I be added please 🙏🏼