iiinova — where your digital self keeps evolving

Martin Pacesa @martinpacesa.bsky.social · 21/09/2026

And ʙɪɴᴅᴄʀᴀꜰᴛ2 is for everyone: we've teamed up with @adaptyv.bio, AriaX Bio & Tamarind Bio to host it, so anyone can run it without a GPU. Built by @erikmaeots.bsky.social, @liza-ch.bsky.social , Leonardo Tredese & Jan Dernic. Special thanks to @sokrypton.org & Lennart Nickel. 🚀

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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026

What we're most excited about: multi-target optimisation. One binder against several targets, with detargeting to avoid off-targets and paralogs. Lennart Nickel and Paul Kittner release a complementary cross-species approach that plugs onto BC1 for existing workflows. github.com/martinpacesa...

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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026

We built a custom integrated engine that makes ʙɪɴᴅᴄʀᴀꜰᴛ2 dramatically faster than v1. And it isn't limited to structured domains: you can target disordered regions, short linear motifs, or a target given as a bare sequence.

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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026

ʙɪɴᴅᴄʀᴀꜰᴛ2 now designs almost any binder format: • mini & large binders • linear & cyclic peptides • VHHs, scFvs & Fabs • ankyrin repeat proteins (ARPs) • homo-oligomers & multidomain binders • induced-fit & fold-switch binders

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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

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Martin Pacesa @martinpacesa.bsky.social · 04/08/2026

We are looking for a lab manager starting from January 2027, you can find more information on our members page pacesalab.com#members. We are also starting to look into hosting master students starting 2027.

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Martin Pacesa @martinpacesa.bsky.social · 11/07/2026

The fold complexity scoring game has been updated with additional aspects of protein complexity according to suer feedback! All the scores have been recalculated and at least to me seem to correlate better with the apparent complexity of the fold! Happy voting!

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Martin Pacesa @martinpacesa.bsky.social · 08/07/2026

Lots of votes already! Thank you everyone! I have again updated the set of structures based on the great feedback from people. You should have an easier time voting now and it includes more interesting structures.

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Martin Pacesa @martinpacesa.bsky.social · 08/07/2026

First update and score calibration, seems the base metric only agrees with humans 73.5% of the time! I have updated the set of structures which should make it more intuitive to vote. Hopefully we can improve the metric to a better agreement!

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Martin Pacesa @martinpacesa.bsky.social · 07/07/2026

There are currently several components based on human estimation of what makes a complex protein fold. Please send us feedback if you think we are missing something or currently severely underestimating one of the factors! Happy voting!

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Martin Pacesa @martinpacesa.bsky.social · 07/07/2026

We have also added a subsample of 1000 protein chains form the PDB to help better calibrate the metric and see if one protein feels complex enough, relative to other folds. This will be updated weekly to account for your votes, until we reach a good value.

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Martin Pacesa @martinpacesa.bsky.social · 07/07/2026

We often talk about complex protein folds but what does that really mean? Turns out we don't have a good metric for it. So we made a game to make one! Head over to our website to vote on which fold you think is more complex and why! pacesalab.com/foldcomplexi...

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Martin Pacesa @martinpacesa.bsky.social · 15/06/2026

My favourite sequential folding video, featured on the homepage

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Martin Pacesa @martinpacesa.bsky.social · 15/06/2026

Lastly, I want to give massive credit to @bradyajohnston.bsky.social , who built Molecular Nodes, and made it possible to generate such beautiful renderings for the website.

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Martin Pacesa @martinpacesa.bsky.social · 15/06/2026

We also have a page on BindCraft, where we describe what it can and cannot do currently, and list publications that have experimentally validated BindCraft-designed binders already.

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Martin Pacesa @martinpacesa.bsky.social · 15/06/2026

We have a page for resources where you can find some online tools we have built that everyone can use (such as the Matthew probability calculator), as well es editable PDF figures from some of our papers to use for your own figures.

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Martin Pacesa @martinpacesa.bsky.social · 15/06/2026

Our lab website is finally online! pacesalab.com You can find information about our research, publications, and on-going developments in the lab.

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Martin Pacesa @martinpacesa.bsky.social · 29/04/2026

I am happy to share a review I recently wrote on the design of peptide binders. It gives an overview of experimentally validated tools and discusses the challenges of why peptide design is more difficult than the design of classical protein binders. www.chimia.ch/chimia/artic...

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Martin Pacesa @martinpacesa.bsky.social · 28/04/2026

Extremely excited about the results of @adaptyv.bio RBX1 binder design competition! 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕2 performed very well, with 3 out of 7 designs binding to the disordered tail. Overall, only 9 binders worked out of 322 tested, 2.8% hit rate! Proud of the BC2 team ♥️ (Erik, Liza, Leo)

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Martin Pacesa @martinpacesa.bsky.social · 04/03/2026

Almost forgot to brag about the absolutely amazing office the UZH Insitute of Pharmacology has provided for me ♥️ Protein structural art by Francisco Enguita (www.behance.net/fenguita)

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Martin Pacesa @martinpacesa.bsky.social · 03/03/2026

2026 has been a remarkable year for me so far (despite the current world events): opening my lab at the University of Zurich, assembling an amazing group of people in the group, and celebrating it with a fantastic lab warming party. Figured it's also time for a small profile refresh.

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Martin Pacesa @martinpacesa.bsky.social · 22/01/2026

Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.

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Martin Pacesa @martinpacesa.bsky.social · 30/12/2025

Fully circular double rainbow appeared today while snowboarding

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Martin Pacesa @martinpacesa.bsky.social · 28/10/2025

In addition to that, we had the amazing opportunity to speak with Lennart in Zacatecas along the whole Mexican biochemistry community, such an incredible venue and great community of scientists. Thanks to Jose A. Farias Rico for inviting us!!!

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Martin Pacesa @martinpacesa.bsky.social · 28/10/2025

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 🖥️

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Martin Pacesa @martinpacesa.bsky.social · 09/10/2025

All that my office requires for now is a good tea preparation station

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Martin Pacesa @martinpacesa.bsky.social · 01/10/2025

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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Martin Pacesa @martinpacesa.bsky.social · 27/08/2025

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 · 27/08/2025

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 · 27/08/2025

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 · 27/08/2025

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 · 07/08/2025

"Hey Bob, just dock the AF3 prediction into density and deposit"

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Martin Pacesa @martinpacesa.bsky.social · 25/07/2025

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

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Martin Pacesa @martinpacesa.bsky.social · 23/07/2025

#ACA2025 such a blast! Great to meet with my old lab mate Justin Flatt (now at RCSB) and @cdsnow.bsky.social !

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Martin Pacesa @martinpacesa.bsky.social · 30/06/2025

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design! github.com/martinpacesa...

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Martin Pacesa @martinpacesa.bsky.social · 06/06/2025

Boltz2 has dropped with possibility to predict ligand affinities. However, the mixed biochemical metrics (Kd, Ki, IC50 from different sources) used for training the module are concerning bit.ly/boltz2-pdf

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Martin Pacesa @martinpacesa.bsky.social · 09/04/2025

Amazing talk by Jimi Olaghere sharing his story of receiving the Casgevy treatment and how it improved his life with sickle cell disease ! #CRISPRMED25

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Martin Pacesa @martinpacesa.bsky.social · 23/03/2025

What an amazing experience to be at the 76th Mosbacher kolloquim! Awesome talks on protein design and structural biology and a lot of conceptual discussions on where the field is going. Glad to also have been able to present our poster on binder design using BindCraft!

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Martin Pacesa @martinpacesa.bsky.social · 17/03/2025

What all people look like to Noelia

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Martin Pacesa @martinpacesa.bsky.social · 13/03/2025

Spending the next weeks depositing all my cryo datasets into the EMPIAR database as raw movies. First two are almost done!

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Martin Pacesa @martinpacesa.bsky.social · 21/01/2025

Novel phage-derived Cas12 system discovered that interacts with E.coli Thioredoxin and regulates its activity. www.biorxiv.org/content/10.1... P.S.: Not digging the name

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Martin Pacesa @martinpacesa.bsky.social · 19/01/2025

For BindCraft v2 most people would like to see binder maturation to be implemented, and also do a youtube tutorial on how to run BindCraft. All in the works!

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Martin Pacesa @martinpacesa.bsky.social · 19/01/2025

Most users are happy with the way the pipeline runs and 2/3rds of users got satisfactory binder designs, which is a great turn out.

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Martin Pacesa @martinpacesa.bsky.social · 19/01/2025

We processed the results of the BindCraft user experience poll and we are quite happy with how it turned out. We had over 60 responses from many different users, turns about about a quarter are from industry and a quarter of users run it via Google Colab!

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