Martin Pacesa
@martinpacesa.bsky.social
Structural biologist working on 🖥️ protein design, machine learning🤖, crystallography💎, and cryoEM🔬. Avid weirdness connoisseur 🎩
Reposted by Martin Pacesa
ProteinCHAOS runs entirely in the browser and lets you choose how to visualize your protein structures.
It supports PDB files from the PDB and AlphaFold servers and offers several visual themes so you can "paint" abstract art with protein traces. I hope it helps you create some interesting images!
It supports PDB files from the PDB and AlphaFold servers and offers several visual themes so you can "paint" abstract art with protein traces. I hope it helps you create some interesting images!
November 23, 2025 at 11:18 PM
ProteinCHAOS runs entirely in the browser and lets you choose how to visualize your protein structures.
It supports PDB files from the PDB and AlphaFold servers and offers several visual themes so you can "paint" abstract art with protein traces. I hope it helps you create some interesting images!
It supports PDB files from the PDB and AlphaFold servers and offers several visual themes so you can "paint" abstract art with protein traces. I hope it helps you create some interesting images!
Reposted by Martin Pacesa
POV: you are a young woman celebrating a recent academic success
November 17, 2025 at 7:20 PM
POV: you are a young woman celebrating a recent academic success
Reposted by Martin Pacesa
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
Filament formation and NAD processing by noncanonical human FAM118 sirtuins
Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...
rdcu.be
November 17, 2025 at 11:37 AM
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
Very happy to be this year’s recipient of the 𝗣𝗲𝘁𝗲𝗿 𝗮𝗻𝗱 𝗧𝗿𝗮𝘂𝗱𝗹 𝗘𝗻𝗴𝗲𝗹𝗵𝗼𝗿𝗻 𝗙𝗼𝘂𝗻𝗱𝗮𝘁𝗶𝗼𝗻 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗔𝘄𝗮𝗿𝗱 together with @jenspuschhof.bsky.social
www.engelhorn-stiftung.de/forschungspr...
www.engelhorn-stiftung.de/forschungspr...
FORSCHUNGSPREIS — Peter&TraudlEngelhornStiftung
www.engelhorn-stiftung.de
November 14, 2025 at 12:20 PM
Very happy to be this year’s recipient of the 𝗣𝗲𝘁𝗲𝗿 𝗮𝗻𝗱 𝗧𝗿𝗮𝘂𝗱𝗹 𝗘𝗻𝗴𝗲𝗹𝗵𝗼𝗿𝗻 𝗙𝗼𝘂𝗻𝗱𝗮𝘁𝗶𝗼𝗻 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗔𝘄𝗮𝗿𝗱 together with @jenspuschhof.bsky.social
www.engelhorn-stiftung.de/forschungspr...
www.engelhorn-stiftung.de/forschungspr...
Reposted by Martin Pacesa
The Center for Microscopy and Image Analysis at the University of Zurich is seeking a new Head:
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
UZH: Head of the Center for Microscopy and Image Analysis (Core Facility)
The Center for Microscopy and Image Analysis (ZMB) is a nationally and internationally recognized Core Facility at the University of Zurich (UZH), providing access to state-of-the-art light and electr...
jobs.uzh.ch
November 12, 2025 at 6:42 PM
The Center for Microscopy and Image Analysis at the University of Zurich is seeking a new Head:
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
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...