Martin Pacesa
@martinpacesa.bsky.social
Structural biologist working on 🖥️ protein design, machine learning🤖, crystallography💎, and cryoEM🔬. Avid weirdness connoisseur 🎩
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!!!
October 28, 2025 at 11:53 PM
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!!!
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 🖥️
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!
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.
August 27, 2025 at 8:52 PM
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.
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!
August 27, 2025 at 4:14 PM
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!
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.
August 27, 2025 at 4:14 PM
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.
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...
"Hey Bob, just dock the AF3 prediction into density and deposit"
August 7, 2025 at 5:04 PM
"Hey Bob, just dock the AF3 prediction into density and deposit"
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!
July 25, 2025 at 7:48 AM
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!
#ACA2025 such a blast! Great to meet with my old lab mate Justin Flatt (now at RCSB) and @cdsnow.bsky.social !
July 23, 2025 at 3:15 AM
#ACA2025 such a blast! Great to meet with my old lab mate Justin Flatt (now at RCSB) and @cdsnow.bsky.social !
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...
github.com/martinpacesa...
June 30, 2025 at 7:45 PM
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...
github.com/martinpacesa...
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
bit.ly/boltz2-pdf
June 6, 2025 at 1:47 PM
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
bit.ly/boltz2-pdf
Amazing talk by Jimi Olaghere sharing his story of receiving the Casgevy treatment and how it improved his life with sickle cell disease ! #CRISPRMED25
April 9, 2025 at 12:10 PM
Amazing talk by Jimi Olaghere sharing his story of receiving the Casgevy treatment and how it improved his life with sickle cell disease ! #CRISPRMED25
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!
March 23, 2025 at 12:14 PM
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!
What all people look like to Noelia
March 17, 2025 at 8:11 AM
What all people look like to Noelia
Spending the next weeks depositing all my cryo datasets into the EMPIAR database as raw movies. First two are almost done!
March 13, 2025 at 2:29 PM
Spending the next weeks depositing all my cryo datasets into the EMPIAR database as raw movies. First two are almost done!
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
www.biorxiv.org/content/10.1...
P.S.: Not digging the name
January 21, 2025 at 1:34 PM
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
www.biorxiv.org/content/10.1...
P.S.: Not digging the name
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!
January 19, 2025 at 12:15 PM
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!
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.
January 19, 2025 at 12:15 PM
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.
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!
January 19, 2025 at 12:15 PM
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!
This N2 tank is begging for help
January 9, 2025 at 1:32 PM
This N2 tank is begging for help
We also added the option to predict MPNN-optimised designs with initial guess (a la Bennett et al. 2023) and big bang (a la Schweke et al. 2023). This significantly improves design success for hard targets.
December 30, 2024 at 9:35 PM
We also added the option to predict MPNN-optimised designs with initial guess (a la Bennett et al. 2023) and big bang (a la Schweke et al. 2023). This significantly improves design success for hard targets.
What’s new in this version? Aside from some bug fixes, we adjusted the default settings so that user defined hotspots are now respected better than before, and designs target the defined binding site.
December 30, 2024 at 9:35 PM
What’s new in this version? Aside from some bug fixes, we adjusted the default settings so that user defined hotspots are now respected better than before, and designs target the defined binding site.