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Martin Pacesa @martinpacesa.bsky.social · 4d

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Martin Pacesa @martinpacesa.bsky.social · 6d

😁 it’s a hawaiian shirt I got on my last day in Correia lab and I promised I would wear it on my first day in the new job

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Martin Pacesa @martinpacesa.bsky.social · 7d

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!

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Reposted by Martin Pacesa

Luuk Loeff @lloeff.bsky.social · 9d

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...

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

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Martin Pacesa @martinpacesa.bsky.social · 9d

Congratulations Tina!!

Martin Pacesa @martinpacesa.bsky.social · 15d

Very nice

Martin Pacesa @martinpacesa.bsky.social · Sep 5

Very nice!

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Reposted by Martin Pacesa

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · Sep 5

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/...

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Martin Pacesa @martinpacesa.bsky.social · Sep 5

Thank you kindly Malcolm!

Martin Pacesa @martinpacesa.bsky.social · Sep 4

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!

European Research Council (ERC) @erc.europa.eu · Sep 4

📣 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

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Reposted by Martin Pacesa

Sorek Lab @soreklab.bsky.social · Sep 2

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
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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

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Reposted by Martin Pacesa

Daan C. Swarts @dcswarts.bsky.social · Aug 28

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.

Martin Pacesa @martinpacesa.bsky.social · Aug 27

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...

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

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...

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

I often barely believe it. Recently we've also been having a lot of luck with single digit nanomolar affinities. This is affinity range distribution from our latest campaign, 42 screened, 22 binders, almost all low nanomolar, some picomolar.

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

Thank you!

Martin Pacesa @martinpacesa.bsky.social · Aug 27

❤️

Reposted by Martin Pacesa

Torsten Schwede @torstenschwede.bsky.social · Aug 27

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

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CAMEO-3D @cameo3d.org · Aug 27

🔬 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.

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

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

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Reposted by Martin Pacesa

Fay Lin @faylinphd.bsky.social · Aug 27

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...

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

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

❤️

Reposted by Martin Pacesa

Vince Luca, PhD @thelucalab.bsky.social · Aug 27

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.

Martin Pacesa @martinpacesa.bsky.social · Aug 27

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...

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

We plan to keep developing open source and user friendly software in the future, to put research tools into everyone's hands. You can find the easily installable BindCraft code on GitHub
github.com/martinpacesa...

GitHub - martinpacesa/BindCraft: User friendly and accurate binder design pipeline

User friendly and accurate binder design pipeline. Contribute to martinpacesa/BindCraft development by creating an account on GitHub.

github.com

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

I cannot describe how overwhelmed we were with the adoption of BindCraft within the community, we received so much feedback, particularly from non-experts designers, as well as their own success stories in binder design and it is absolutely amazing it see!

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

Since the preprint we have included more bioinformatics analysis, such as novelty of designed folds and interfaces. We also compare computational efficiency and interface amino acid composition to RFdiffusion binders.

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

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...

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