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Max Fürst

@maxfus.bsky.social

1.8K followers 980 following 380 posts

www.fuerstlab.com

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Max Fürst @maxfus.bsky.social · May 20

🚨 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 🧵👇🏽

Overview of ADD-tagging including ADP-ribosyl cyclase (ADPRC)-catalysed dinucleotide substrate generation and two step chemoenzymatic labelling of target proteins with the flavin transferase ApbE, followed by click chemistry-based functional group attachment.

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Max Fürst @maxfus.bsky.social · 2d

youtu.be/Q_oFL_b719g?...

You Don't Own Me - Bette Midler, Goldie Hawn & Diane Keaton

YouTube video by decay21450

youtu.be

Max Fürst @maxfus.bsky.social · 2d

also, this editorial's answer to the question is yes (in violation of Betteridge's law), recommending to just don't produce AI slob that doesn't add anything

Max Fürst @maxfus.bsky.social · 2d

can't find the article now, but I saw a very useful graph once w/ # of articles vs # of reviews in a field:
-many articles, few reviews: write review
-few articles, many reviews: write review of reviews
-many articles, many reviews: write specialized review
-few articles, few reviews: write proposal

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Reposted by Max Fürst

Prof. Sam Lawler @sundogplanets.mastodon.social.ap.brid.gy · 5d

It's becoming increasingly clear to me that Reflect Orbital's fucking stupid giant mirror satellite, with absolutely NOTHING useful to offer, which will cause countless safety issues, ecological disasters, and destroy the night sky, is going to launch.

A bunch of astronomers and I have sent out […]

Original post on mastodon.social

mastodon.social

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Reposted by Max Fürst

Sikkom @sikkom.bsky.social · 4d

Groen licht voor grote AI-fabriek in Groningen. Europa investeert 71 miljoen euro

De kogel is door de oude tabaksfabriek: Groningen krijgt een grote AI-fabriek. De Europese Commissie gaat 71 miljoen euro investeren. Het benodigde bedrag van 200 miljoen is daardoor bij elkaar.

dlvr.it

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Reposted by Max Fürst

SusanK @susankleinfelter.bsky.social · 5d

Woohoo! Go Foldit!

Structural Biology @actacrystd.iucr.org · 5d

Andreas C. Petrides et al.: Reconstructing biological molecules with help from video gamers ##Foldit##PDBREDO##CitizenScience@umassd...##IUCrhttps://journals.iucr.org/paper?S2059798325008149

Reconstructing biological molecules with help from video gamers

The results of the Foldit citizen science puzzles for crystallographic models and their integration into the PDB-REDO databank are discussed.

journals.iucr.org

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Max Fürst @maxfus.bsky.social · 6d

Maxim could you kindly clarify: did you actually recompute all the structures, or are the models identical to the previous AFDB version? And are the MSAs the ones from back in day, or do these reflect more recent db searches? If new predictions were made - with which AF version?

Max Fürst @maxfus.bsky.social · 6d

Great post! In agree that complexity is underestimated, lack of knowledge the bottleneck to design, & intuition key to success. Likely, AI can work work around some, but not all of the issues without explicit data.
Do you mind sharing what pockets you think work better than others with bindcraft?

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Max Fürst @maxfus.bsky.social · 6d

Have you found the entire db MSA data as a dump yet?

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Max Fürst @maxfus.bsky.social · 6d

Ooohh providing the MSAs is wonderful. Will the data be in a new Google cloud bucket? Is it already available?

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Reposted by Max Fürst

EMBL-EBI @ebi.embl.org · 7d

We’re renewing our collaboration with Google DeepMind!

We'll keep developing the AlphaFold Database to support protein science worldwide 🎉

To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.

www.ebi.ac.uk/about/news/t...

🖥️🧬 #AlphaFold
@pdbeurope.bsky.social

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Max Fürst @maxfus.bsky.social · 8d

For sure. I'm not downplaying the breakthrough itself. But I do think the other, dependent achievements would not never have come. How much later - who knows.

Reposted by Max Fürst

AI x Bio Discovery @aixbiobot.bsky.social · 8d

Mapping the evolution of computationally designed protein binders [new]
Evolve comp. mini-protein binders *in vivo*. Maps seq-affinity.

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Max Fürst @maxfus.bsky.social · 8d

Agree they should get the Nobel, but if it hadn't been that synthetic route, another one would've eventually come, good enough at least to make primers. Or we would've dugged earlier deeper into primases or protein priming. Oh wait, guess maybe we wouldn't have been able to study those without PCR 🤔

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Max Fürst @maxfus.bsky.social · 9d

Un-frigging-believable. I have waited for something like this for so long!

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Max Fürst @maxfus.bsky.social · 10d

Wait but that's inconveniently more complex and (😱) mathy, my 1st years will not be happy

Di Jiang @dijiang319.bsky.social · Sep 12

@science.org ⤵️challenges prevailing notion—repressor and activator act by distinct mechanisms: repressors block via steric hindrance/activators enable Pol II binding to promoter🧬

E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism | Science bit.ly/adv2064

Reposted by Max Fürst

Di Jiang @dijiang319.bsky.social · Sep 12

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Reposted by Max Fürst

AI x Bio Discovery @aixbiobot.bsky.social · 16d

The AlphaFold Database Ages [updated]
AlphaFold DB:
...needs updating as entries conflict with newer UniProt releases, showing bioinformatics databases' rapid obsolescence.

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Reposted by Max Fürst

Simon Dürr @simonduerr.eu · 19d

We are hiring a PhD student 🎓

Work with me and Matthias Rüdt in our department on an exciting industry collaboration with Lonza combining high-throughput experiments and molecular modelling using AlphaFold and MolecularDynamics

📍 Sion, Valais, Switzerland

More info: www.jobup.ch/fr/emplois/d...

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Reposted by Max Fürst

Danielle Navarro @djnavarro.blacksky.app · 23d

Against my better instincts, I have written some notes on how human probability judgements work and what you should expect from surveys that ask people to guess what proportion of the population is transgender. I hope never to speak of this matter again

Some notes on probability judgement – Notes from a data witch

For the love of fuck, literally nobody thinks that 20% of the population is transgender. Please stop sharing that ridiculous YouGov statistic

blog.djnavarro.net

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Max Fürst @maxfus.bsky.social · 23d

Finding enzyme homologs with beneficial properties, may often be relatively close in sequence space. Can largely address problem by plugging a sequence search after foldseek, but makes mining pipelines more complex.
If UI limitation, maybe as an a3m dump-only option for full AFDB or higher % clust?

Max Fürst @maxfus.bsky.social · 23d

Given the performance improvements, is a foldseek server searching the full AFDB conceivable? Would be very useful for e.g. for enzyme mining and hard to implement locally.

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Max Fürst @maxfus.bsky.social · 23d

Maybe. Or, there is now such a fierce competition driven by commercial interests that pushes publications to happen at that rate. But is there still time for anyone to seriously scrutinize & compare the models and is able to keep track on what constitutes a major advance and what's a lot of smoke?

Max Fürst @maxfus.bsky.social · 24d

They should just strike a deal with nature, until version 10, all models get directly uploaded to nature.com instead of biorxiv.org

Max Fürst @maxfus.bsky.social · 24d

And how is Baker lab organising this internally? "OK, you guys work on RFd2. Meanwhile, you others guys enjoy the long weekend, when you're back you start work on RFd3"
Or are we now in a state where we can conceptualise, code, train, benchmark, test, and write on a new frontier model in 5 months?

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