Martin Pacesa
@martinpacesa.bsky.social
Structural biologist working on 🖥️ protein design, machine learning🤖, crystallography💎, and cryoEM🔬. Avid weirdness connoisseur 🎩
Reposted by Martin Pacesa
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology
An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.
www.nature.com
November 6, 2025 at 1:49 PM
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
Reposted by Martin Pacesa
With the US government absent from the COP30 global climate summit, it will be up to others to avert catastrophe
go.nature.com/4ofcrH6
go.nature.com/4ofcrH6
How to fight climate change without the US: a guide to global action
With the US government absent from the COP30 global climate summit, it will be up to others to avert catastrophe.
go.nature.com
November 3, 2025 at 4:59 PM
With the US government absent from the COP30 global climate summit, it will be up to others to avert catastrophe
go.nature.com/4ofcrH6
go.nature.com/4ofcrH6
So exciting to be able to do a binder design workshop using BindCraft in Mexico 🇲🇽, with such a fantastic community of scientists! The designs to probe interesting biological problems looked amazing! The GPU compute was very generously provided by @aaronmring.bsky.social and AriaX.bio 🖥️
October 28, 2025 at 11:53 PM
So exciting to be able to do a binder design workshop using BindCraft in Mexico 🇲🇽, with such a fantastic community of scientists! The designs to probe interesting biological problems looked amazing! The GPU compute was very generously provided by @aaronmring.bsky.social and AriaX.bio 🖥️
Reposted by Martin Pacesa
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Reposted by Martin Pacesa
BIG BIG congratulations to our PhD student
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
October 25, 2025 at 12:44 AM
BIG BIG congratulations to our PhD student
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
Reposted by Martin Pacesa
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
October 20, 2025 at 11:26 AM
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
Reposted by Martin Pacesa
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
blog.genesmindsmachines.com
October 7, 2025 at 4:11 PM
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
Reposted by Martin Pacesa
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 Martin Pacesa
Skeetorial on our BRAF preprint!
tinyurl.com/asymmBRAF
The RAS->RAF->MEK->ERK cascade carries mutations in most human cancers. Interestingly, although we have three RAF paralogues (A, B and C), it is the BRAF that is predominantly mutated in cancer patients. (1/10)
tinyurl.com/asymmBRAF
The RAS->RAF->MEK->ERK cascade carries mutations in most human cancers. Interestingly, although we have three RAF paralogues (A, B and C), it is the BRAF that is predominantly mutated in cancer patients. (1/10)
Mechanism of MEK1 phosphorylation by the N-terminal acidic motif-mediated asymmetric BRAF dimer
The RAF/MEK/ERK signaling cascade regulates cell proliferation and differentiation and is frequently dysregulated in cancer. Approximately 90% of RAF-mutant cancers harbour mutations in B-type of Rapi...
tinyurl.com
October 14, 2025 at 8:17 AM
Skeetorial on our BRAF preprint!
tinyurl.com/asymmBRAF
The RAS->RAF->MEK->ERK cascade carries mutations in most human cancers. Interestingly, although we have three RAF paralogues (A, B and C), it is the BRAF that is predominantly mutated in cancer patients. (1/10)
tinyurl.com/asymmBRAF
The RAS->RAF->MEK->ERK cascade carries mutations in most human cancers. Interestingly, although we have three RAF paralogues (A, B and C), it is the BRAF that is predominantly mutated in cancer patients. (1/10)
Reposted by Martin Pacesa
Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org
🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters
🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters
October 13, 2025 at 3:45 PM
Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org
🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters
🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters
Reposted by Martin Pacesa
Any structural biologists who want some fun? Try building mirror folds. When you’re building them you seriously innately feel like this is “off” but they do exist! When I looked at some of these datasets and deciding which way to turn in Coot it was so offsetting www.biorxiv.org/content/10.1...
October 13, 2025 at 5:05 PM
Any structural biologists who want some fun? Try building mirror folds. When you’re building them you seriously innately feel like this is “off” but they do exist! When I looked at some of these datasets and deciding which way to turn in Coot it was so offsetting www.biorxiv.org/content/10.1...
Reposted by Martin Pacesa
All that my office requires for now is a good tea preparation station
October 9, 2025 at 9:31 AM
All that my office requires for now is a good tea preparation station
Super happy to start my new position back at the beautiful University Zurich Irchel campus. Will spend some time building up the lab, and then jump into doing some super cool science very soon!
October 1, 2025 at 4:00 PM
Super happy to start my new position back at the beautiful University Zurich Irchel campus. Will spend some time building up the lab, and then jump into doing some super cool science very soon!
Reposted by Martin Pacesa
Hiring! 🧬🔬
Ever wondered how bacteria fight off viruses? We’re looking for a PhD student to dive into the molecular basis of newly discovered microbial immune systems, an area of biology where much remains to be uncovered.
RT/share to help us find our next team member!
www.lumc.nl/en/about-lum...
Ever wondered how bacteria fight off viruses? We’re looking for a PhD student to dive into the molecular basis of newly discovered microbial immune systems, an area of biology where much remains to be uncovered.
RT/share to help us find our next team member!
www.lumc.nl/en/about-lum...
PhD-positie Bacteriële Verdedigingssystemen tegen Virussen | LUMC
Wij zoeken een getalenteerde en gemotiveerde PhD-kandidaat om het onderzoeksteam van Luuk Loeff te versterken. In dit project maak je gebruik van geavanceerde technologieën om te ontrafelen hoe bacter...
www.lumc.nl
September 29, 2025 at 11:36 AM
Hiring! 🧬🔬
Ever wondered how bacteria fight off viruses? We’re looking for a PhD student to dive into the molecular basis of newly discovered microbial immune systems, an area of biology where much remains to be uncovered.
RT/share to help us find our next team member!
www.lumc.nl/en/about-lum...
Ever wondered how bacteria fight off viruses? We’re looking for a PhD student to dive into the molecular basis of newly discovered microbial immune systems, an area of biology where much remains to be uncovered.
RT/share to help us find our next team member!
www.lumc.nl/en/about-lum...
Reposted by Martin Pacesa
In 2019, we published a clustering & nomenclature of beta turns in proteins & found 18 unique types. The code was in python2. I've just rewritten it in python3, because it might still be useful to people.
The paper & code:
journals.plos.org/ploscompbiol...
github.com/DunbrackLab/...
The paper & code:
journals.plos.org/ploscompbiol...
github.com/DunbrackLab/...
September 5, 2025 at 9:48 AM
In 2019, we published a clustering & nomenclature of beta turns in proteins & found 18 unique types. The code was in python2. I've just rewritten it in python3, because it might still be useful to people.
The paper & code:
journals.plos.org/ploscompbiol...
github.com/DunbrackLab/...
The paper & code:
journals.plos.org/ploscompbiol...
github.com/DunbrackLab/...
Really excited to receive the ERC Starting Grant! It’s gonna allow us to do a lot of cool protein design and structural biology method development in the next few years!
📣 The ERC Starting Grant call results are out!
Find out which early-career researchers will receive funding this year, what they will be investigating, where they will be based... plus lots of other #ERCStG facts & figures for 2025!
➡️ buff.ly/IsafuFh
#FrontierResearch 🇪🇺#EUfunded #HorizonEurope
Find out which early-career researchers will receive funding this year, what they will be investigating, where they will be based... plus lots of other #ERCStG facts & figures for 2025!
➡️ buff.ly/IsafuFh
#FrontierResearch 🇪🇺#EUfunded #HorizonEurope
September 4, 2025 at 10:23 AM
Really excited to receive the ERC Starting Grant! It’s gonna allow us to do a lot of cool protein design and structural biology method development in the next few years!
Reposted by Martin Pacesa
Preprint: De-novo design of proteins that inhibit bacterial defenses
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
www.biorxiv.org
September 2, 2025 at 10:48 AM
Preprint: De-novo design of proteins that inhibit bacterial defenses
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Reposted by Martin Pacesa
BindCraft can be used to design synthetic protein binders with incredible accuracy and success rate - Out now in Nature.
BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.
BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 28, 2025 at 9:03 AM
BindCraft can be used to design synthetic protein binders with incredible accuracy and success rate - Out now in Nature.
BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.
BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.
We also wrote a little Behind the paper blog post with Lennart and Christian. It gives some idea on what our motivation was behind developing BindCraft and why we chose this particular set of target proteins to work on 🙂
communities.springernature.com/posts/behind...
communities.springernature.com/posts/behind...
August 27, 2025 at 9:13 PM
We also wrote a little Behind the paper blog post with Lennart and Christian. It gives some idea on what our motivation was behind developing BindCraft and why we chose this particular set of target proteins to work on 🙂
communities.springernature.com/posts/behind...
communities.springernature.com/posts/behind...
Reposted by Martin Pacesa
Critical benchmarking of structure prediction methods has been crucial for measuring progress and detecting breakthroughs. But how will the future look like? Join the discussion at our workshop in Basel on September 8 - just before the [BC]2 conference.
@sib.swiss @biozentrum.unibas.ch
⬇️⬇️⬇️
@sib.swiss @biozentrum.unibas.ch
⬇️⬇️⬇️
🔬 Workshop: Future of Structure Prediction Benchmarking
📅 Sept 8, 2025 | Basel
💡 Talks + breakout sessions on #CASP #CAPRI #CAMEO & benchmarking for drug discovery
🎟️ Free registration (limited spots): lu.ma/ws9nu1xf
Join us to explore how benchmarking can drive breakthroughs in structure prediction.
📅 Sept 8, 2025 | Basel
💡 Talks + breakout sessions on #CASP #CAPRI #CAMEO & benchmarking for drug discovery
🎟️ Free registration (limited spots): lu.ma/ws9nu1xf
Join us to explore how benchmarking can drive breakthroughs in structure prediction.
The future of structure prediction benchmarking: measuring progress and breakthroughs · Luma
Benchmarking has been a key driver of progress in protein structure prediction methods. As the field continues to evolve, several key questions prevail:
How…
lu.ma
August 27, 2025 at 5:32 PM
Critical benchmarking of structure prediction methods has been crucial for measuring progress and detecting breakthroughs. But how will the future look like? Join the discussion at our workshop in Basel on September 8 - just before the [BC]2 conference.
@sib.swiss @biozentrum.unibas.ch
⬇️⬇️⬇️
@sib.swiss @biozentrum.unibas.ch
⬇️⬇️⬇️
Reposted by Martin Pacesa
BindCraft is now published in @nature.com!
The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens.
Read more at GEN:
www.genengnews.com/topics/artif...
The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens.
Read more at GEN:
www.genengnews.com/topics/artif...
BindCraft AI Model Achieves One-Shot Functional Protein Design
The open-source pipeline designs proteins with improved success rates for therapeutic targets, including gene editing proteins and allergens.
www.genengnews.com
August 27, 2025 at 4:55 PM
BindCraft is now published in @nature.com!
The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens.
Read more at GEN:
www.genengnews.com/topics/artif...
The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens.
Read more at GEN:
www.genengnews.com/topics/artif...
Reposted by Martin Pacesa
Bindcraft is awesome! If you haven’t already seen the preprint check out the final pub here. We’ve had nearly 100% success using it for the targets we’ve attempted.
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:46 PM
Bindcraft is awesome! If you haven’t already seen the preprint check out the final pub here. We’ve had nearly 100% success using it for the targets we’ve attempted.
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Since when are vaults cool again? Loving it
Structural flexibility of the human vault protein revealed by high-resolution cryo-EM and molecular dynamics simulations https://www.biorxiv.org/content/10.1101/2025.08.26.672097v1
August 27, 2025 at 10:49 AM
Since when are vaults cool again? Loving it