Max Fürst
@maxfus.bsky.social
Asst. Prof. Uni Groningen 🇳🇱
Comp & Exp Biochemist, Protein Engineer, 'Would-be designer' (F. Arnold) | SynBio | HT Screens & Selections | Nucleic Acid Enzymes | Biocatalysis | Rstats & Datavis
https://www.fuerstlab.com
https://orcid.org/0000-0001-7720-9
Comp & Exp Biochemist, Protein Engineer, 'Would-be designer' (F. Arnold) | SynBio | HT Screens & Selections | Nucleic Acid Enzymes | Biocatalysis | Rstats & Datavis
https://www.fuerstlab.com
https://orcid.org/0000-0001-7720-9
Pinned
Max Fürst
@maxfus.bsky.social
· Dec 16
New preprint🚨
Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design?
What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be?
Why to be wary🧵👇
Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design?
What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be?
Why to be wary🧵👇
Reposted by Max Fürst
Want to get the data out of a PDF figure? As in, the actual data – not a rough trace-along-the-lines version?
I made an app you might like: adamkucharski.github.io/pdf2plot/
It all started a few years ago... 🧵
I made an app you might like: adamkucharski.github.io/pdf2plot/
It all started a few years ago... 🧵
January 13, 2026 at 9:12 PM
Want to get the data out of a PDF figure? As in, the actual data – not a rough trace-along-the-lines version?
I made an app you might like: adamkucharski.github.io/pdf2plot/
It all started a few years ago... 🧵
I made an app you might like: adamkucharski.github.io/pdf2plot/
It all started a few years ago... 🧵
The only format worse than pdb is cif
My hot take is that CIF and PDB formats are totally ill-equipped for adequately storing metadata describing how structures get generated and processed, and this problem will get worse as AI agents imbued with structural bioinformatics skills pass these files back and forth
January 9, 2026 at 6:33 PM
The only format worse than pdb is cif
Industrial computational protein engineering position in the south of the Netherlands
synsilico.com/storage/app/...
synsilico.com/storage/app/...
synsilico.com
January 9, 2026 at 7:19 AM
Industrial computational protein engineering position in the south of the Netherlands
synsilico.com/storage/app/...
synsilico.com/storage/app/...
Reposted by Max Fürst
Can we design mutations that bias proteins towards desired conformational states?
Today in @science.org, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.
Today in @science.org, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.
Computational design of conformation-biasing mutations to alter protein functions
Conformational biasing (CB) is a rapid and streamlined computational method that uses contrastive scoring by inverse folding models to predict protein variants biased toward desired conformational sta...
www.science.org
January 8, 2026 at 7:08 PM
Can we design mutations that bias proteins towards desired conformational states?
Today in @science.org, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.
Today in @science.org, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.
Reposted by Max Fürst
Today I made a small but momentous start to work in 2026 by changing a single number.
I renamed the file “Papers to write and submit in 2025” to “Papers to write and submit in 2026”.
Stay tuned for more file updates on 1st January 2027.
I renamed the file “Papers to write and submit in 2025” to “Papers to write and submit in 2026”.
Stay tuned for more file updates on 1st January 2027.
January 1, 2026 at 4:26 PM
Today I made a small but momentous start to work in 2026 by changing a single number.
I renamed the file “Papers to write and submit in 2025” to “Papers to write and submit in 2026”.
Stay tuned for more file updates on 1st January 2027.
I renamed the file “Papers to write and submit in 2025” to “Papers to write and submit in 2026”.
Stay tuned for more file updates on 1st January 2027.
Reposted by Max Fürst
1/ Check out our newest paper where we ask: How fast can we experimentally discover binders from scratch?
And we mean scratch: a blinded study.
TLDR: 26 days. And the binders work…and led to new cancer biology.
We’re coming for you AI….
chemrxiv.org/engage/chemr...
And we mean scratch: a blinded study.
TLDR: 26 days. And the binders work…and led to new cancer biology.
We’re coming for you AI….
chemrxiv.org/engage/chemr...
December 26, 2025 at 6:24 PM
1/ Check out our newest paper where we ask: How fast can we experimentally discover binders from scratch?
And we mean scratch: a blinded study.
TLDR: 26 days. And the binders work…and led to new cancer biology.
We’re coming for you AI….
chemrxiv.org/engage/chemr...
And we mean scratch: a blinded study.
TLDR: 26 days. And the binders work…and led to new cancer biology.
We’re coming for you AI….
chemrxiv.org/engage/chemr...
Caught between excitement that "one of us" appears on a major podcast and cringe for parts of the discussion (mainly the self promotion, sadly a hallmark of otherwise enjoyable #hardfork)
Where Is All the A.I.-Driven Scientific Progress?
open.spotify.com
December 30, 2025 at 3:20 PM
Caught between excitement that "one of us" appears on a major podcast and cringe for parts of the discussion (mainly the self promotion, sadly a hallmark of otherwise enjoyable #hardfork)
Reposted by Max Fürst
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Know when to co-fold'em
This is the official web page for the James Fraser Lab at UCSF.
fraserlab.com
December 29, 2025 at 10:25 PM
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Reposted by Max Fürst
So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵
December 26, 2025 at 11:49 PM
So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵
Reposted by Max Fürst
"How can funders avoid crossing the Szilard point?"
The Szilard point is "the threshold at which the total cost of competing for a grant equals (or surpasses) the value of the available funding."
The Szilard point is "the threshold at which the total cost of competing for a grant equals (or surpasses) the value of the available funding."
Point of no returns: researchers are crossing a threshold in the fight for funding
With so little money to go round, the costs of competing for grants can exceed what the grants are worth. When that happens, nobody wins.
www.nature.com
December 19, 2025 at 7:57 AM
"How can funders avoid crossing the Szilard point?"
The Szilard point is "the threshold at which the total cost of competing for a grant equals (or surpasses) the value of the available funding."
The Szilard point is "the threshold at which the total cost of competing for a grant equals (or surpasses) the value of the available funding."
New preprint🚨
Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design?
What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be?
Why to be wary🧵👇
Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design?
What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be?
Why to be wary🧵👇
December 16, 2025 at 3:15 PM
New preprint🚨
Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design?
What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be?
Why to be wary🧵👇
Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design?
What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be?
Why to be wary🧵👇
Fun! Tldr
AI researchers are pissed bc some AI research papers submitted to an AI conference by AI researcher colleagues is AI-written & many are AI-reviewed as found by an AI company's AI model, described in a paper for said AI conference. Said paper was also AI-reviewed (but deffo not AI-written)
AI researchers are pissed bc some AI research papers submitted to an AI conference by AI researcher colleagues is AI-written & many are AI-reviewed as found by an AI company's AI model, described in a paper for said AI conference. Said paper was also AI-reviewed (but deffo not AI-written)
What can researchers do if they suspect that their manuscripts have been peer reviewed using AI?
go.nature.com/4pxUNyD
go.nature.com/4pxUNyD
Major AI conference flooded with peer-reviews written fully by AI
Controversy has erupted after 21% of manuscript reviews for an international AI conference were found to be generated by artificial intelligence.
go.nature.com
November 28, 2025 at 6:51 AM
Fun! Tldr
AI researchers are pissed bc some AI research papers submitted to an AI conference by AI researcher colleagues is AI-written & many are AI-reviewed as found by an AI company's AI model, described in a paper for said AI conference. Said paper was also AI-reviewed (but deffo not AI-written)
AI researchers are pissed bc some AI research papers submitted to an AI conference by AI researcher colleagues is AI-written & many are AI-reviewed as found by an AI company's AI model, described in a paper for said AI conference. Said paper was also AI-reviewed (but deffo not AI-written)
Reposted by Max Fürst
What do you think?
Real SDS-PAGE gel or AI-generated ?
Real SDS-PAGE gel or AI-generated ?
November 26, 2025 at 7:47 AM
What do you think?
Real SDS-PAGE gel or AI-generated ?
Real SDS-PAGE gel or AI-generated ?
We've reached the bizarre state of things where poorly written emails in broken English are the ones that are the most relevant
Students applying for grad school, or reaching out to professors. I have an important piece of advice for you: STOP DOING THIS 👇 (a thread) #STEM #PhD #gradschool #academictips
November 25, 2025 at 7:40 PM
We've reached the bizarre state of things where poorly written emails in broken English are the ones that are the most relevant
Comp. Bio. preAI:
spend days finding (=missing many), understanding (=skimming paper), installing (=missing libs -> bang head), running (=curse hpc queue), & interpreting(=🧐🤔🫣😵💫) output of scientific software
postAI:
spend days trying to talk an AI agent into doing the darn thing for you
spend days finding (=missing many), understanding (=skimming paper), installing (=missing libs -> bang head), running (=curse hpc queue), & interpreting(=🧐🤔🫣😵💫) output of scientific software
postAI:
spend days trying to talk an AI agent into doing the darn thing for you
I know I'm probably using this function all wrong but Gaia/Seqhub really made me cackle today. For your own viewing pleasure, a story in screengrabs 🤣🫣🤖
November 21, 2025 at 6:30 AM
Comp. Bio. preAI:
spend days finding (=missing many), understanding (=skimming paper), installing (=missing libs -> bang head), running (=curse hpc queue), & interpreting(=🧐🤔🫣😵💫) output of scientific software
postAI:
spend days trying to talk an AI agent into doing the darn thing for you
spend days finding (=missing many), understanding (=skimming paper), installing (=missing libs -> bang head), running (=curse hpc queue), & interpreting(=🧐🤔🫣😵💫) output of scientific software
postAI:
spend days trying to talk an AI agent into doing the darn thing for you
Reposted by Max Fürst
#1 lesson I give to protein designers for wet lab purposes : Please design with a Trp and/or multiple Tyr. Please do not design with 10 cysteines.
November 18, 2025 at 1:48 PM
#1 lesson I give to protein designers for wet lab purposes : Please design with a Trp and/or multiple Tyr. Please do not design with 10 cysteines.
Remember when we were on social media because heck how else would we find cool stuff like this
I am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Proteolytic activation of diverse antiviral defense modules in prokaryotes
Linked protease–effector modules are widespread in prokaryotic antiviral defense, yet the mechanisms of most remain poorly understood. Here we show that four of the most prevalent modules—metallo-β-la...
www.biorxiv.org
November 16, 2025 at 12:32 AM
Remember when we were on social media because heck how else would we find cool stuff like this
Reposted by Max Fürst
arXiv will no longer accept review articles and position papers unless they have been accepted at a journal or a conference and complete successful peer review.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
Attention Authors: Updated Practice for Review Articles and Position Papers in arXiv CS Category – arXiv blog
blog.arxiv.org
November 1, 2025 at 5:28 PM
arXiv will no longer accept review articles and position papers unless they have been accepted at a journal or a conference and complete successful peer review.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
Re recent AFDB update, in case you wondered:
- most of AFDB is still same original predictions
-new/changed entries were modeled with AF2
- the MSAs are the originals, so should not contain sequences from last few years
- most of AFDB is still same original predictions
-new/changed entries were modeled with AF2
- the MSAs are the originals, so should not contain sequences from last few years
Yes, only AF2, not AF3. Unchanged models would be the same as 2021, since the settings used here are identical to every release we've had before, and MSAs cached from previous runs for unchanged sequences. Also the sequence databases also remain the same. So the entire db is consistent throughout.
October 23, 2025 at 4:30 PM
Re recent AFDB update, in case you wondered:
- most of AFDB is still same original predictions
-new/changed entries were modeled with AF2
- the MSAs are the originals, so should not contain sequences from last few years
- most of AFDB is still same original predictions
-new/changed entries were modeled with AF2
- the MSAs are the originals, so should not contain sequences from last few years
Reposted by Max Fürst
October 15, 2025 at 9:12 AM
Reposted by Max Fürst
I wrote a blog post about the future of structural bioinformatics.
Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?
Let me know what you think.
jgreener64.github.io/posts/struct...
Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?
Let me know what you think.
jgreener64.github.io/posts/struct...
Where next for structural bioinformatics?
jgreener64.github.io
October 15, 2025 at 2:16 PM
I wrote a blog post about the future of structural bioinformatics.
Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?
Let me know what you think.
jgreener64.github.io/posts/struct...
Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?
Let me know what you think.
jgreener64.github.io/posts/struct...
Reposted by Max Fürst
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 […]
A bunch of astronomers and I have sent out […]
Original post on mastodon.social
mastodon.social
October 9, 2025 at 5:19 PM
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 […]
A bunch of astronomers and I have sent out […]
Reposted by Max Fürst
Groen licht voor grote AI-fabriek in Groningen. Europa investeert 71 miljoen euro
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
October 10, 2025 at 10:13 AM
Groen licht voor grote AI-fabriek in Groningen. Europa investeert 71 miljoen euro