Radoslav Krivak
@rdkbio.bsky.social
🧬 Structural Bioinformatics | 💊 AI/ML for Drug Discovery | Geometric DL
🔬 @iocbprague.bsky.social, prev. PhD @cusbg.bsky.social @mff.unikarlova.cuni.cz
🔬 @iocbprague.bsky.social, prev. PhD @cusbg.bsky.social @mff.unikarlova.cuni.cz
Pinned
Radoslav Krivak
@rdkbio.bsky.social
· Feb 10
How long does it take to predict ligand binding sites for all 220k proteins in the PDB? P2Rank 2.5 does it in 3 hours on a single CPU (16-core amd 5950x)—2x faster than the previous version 🚀.
(1/n)
(1/n)
Reposted by Radoslav Krivak
Very happy @roman-bushuiev.bsky.social and I joined the amazing team led by @hannes-stark.bsky.social to work on BoltzGen, a generative model for binder design based on Boltz-2. Excited what it will enable!
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 27, 2025 at 12:35 PM
Very happy @roman-bushuiev.bsky.social and I joined the amazing team led by @hannes-stark.bsky.social to work on BoltzGen, a generative model for binder design based on Boltz-2. Excited what it will enable!
Reposted by Radoslav Krivak
We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
October 23, 2025 at 1:08 PM
We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
Finally, Mol* with a human face
MolViewSpec: describe, share, and reproduce Mol* molecular scenes with a simple extension
MolViewSpec: a Mol* extension for describing and sharing molecular visualizations
Abstract. Data visualization is a pivotal component of a structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broade
academic.oup.com
September 25, 2025 at 3:24 AM
Finally, Mol* with a human face
Reposted by Radoslav Krivak
September 16, 2025 at 4:48 PM
Reposted by Radoslav Krivak
I am very proud of the final outcome of this project, mainly driven by Corinna Brungs and supported by numerous labs who donated compounds for analysis.
The @pluskal-lab.org is helping colleagues around the world identify unknown compounds.
A #research article about their vast #massspec library has been published in @natmethods.nature.com with Corinna Brungs & @robinschmidt.bsky.social as the first two authors.
See more ► www.uochb.cz/en/news/732
A #research article about their vast #massspec library has been published in @natmethods.nature.com with Corinna Brungs & @robinschmidt.bsky.social as the first two authors.
See more ► www.uochb.cz/en/news/732
September 16, 2025 at 8:25 AM
I am very proud of the final outcome of this project, mainly driven by Corinna Brungs and supported by numerous labs who donated compounds for analysis.
Reposted by Radoslav Krivak
🌿 The Botanical Garden of Charles University’s Faculty of Science turns 250! Founded in 1775, it is one of Central Europe’s oldest university gardens.
Join us for a special anniversary program 15–21 Sept 2025. 🎉
@unikarlova.cuni.cz @botanickazahradauk.bsky.social
Join us for a special anniversary program 15–21 Sept 2025. 🎉
@unikarlova.cuni.cz @botanickazahradauk.bsky.social
September 16, 2025 at 8:22 AM
🌿 The Botanical Garden of Charles University’s Faculty of Science turns 250! Founded in 1775, it is one of Central Europe’s oldest university gardens.
Join us for a special anniversary program 15–21 Sept 2025. 🎉
@unikarlova.cuni.cz @botanickazahradauk.bsky.social
Join us for a special anniversary program 15–21 Sept 2025. 🎉
@unikarlova.cuni.cz @botanickazahradauk.bsky.social
There is a new version of Runs N' Poses preprint by @peterskrinjar.bsky.social and @ninjani.bsky.social comparing Boltz-2 to Boltz-1 and to other co-folding methods by extension (though not yet to classical docking).
@mdc-biocat.bsky.social - how did comparison of Boltz-2 to PocketVina turn out?
@mdc-biocat.bsky.social - how did comparison of Boltz-2 to PocketVina turn out?
With the release of Boltz 2, is there already a review comparing the efficiency of different (new) docking tools? (I’ve already tried Pocket Vina, which is actually quite good for high-throughput)
September 14, 2025 at 4:31 PM
There is a new version of Runs N' Poses preprint by @peterskrinjar.bsky.social and @ninjani.bsky.social comparing Boltz-2 to Boltz-1 and to other co-folding methods by extension (though not yet to classical docking).
@mdc-biocat.bsky.social - how did comparison of Boltz-2 to PocketVina turn out?
@mdc-biocat.bsky.social - how did comparison of Boltz-2 to PocketVina turn out?
Reposted by Radoslav Krivak
YouTube link for MLCB2025 is up! Starting in 30 min. www.youtube.com/live/19I7xTh...
Machine Learning in Computational Biology 2025
YouTube video by Machine Learning in Computational Biology
www.youtube.com
September 10, 2025 at 1:01 PM
YouTube link for MLCB2025 is up! Starting in 30 min. www.youtube.com/live/19I7xTh...
Reposted by Radoslav Krivak
Day 3 opened with Kenneth Atz @Roche tackling the holy grail of #CADD: P-L binding #affinity prediction. By reframing limits of data & models, we can focus on the next solvable challenges - a sharp reminder of complexity & progress ahead.
#CECAM @cecamevents.bsky.social @iocbprague.bsky.social
#CECAM @cecamevents.bsky.social @iocbprague.bsky.social
September 10, 2025 at 9:31 AM
Day 3 opened with Kenneth Atz @Roche tackling the holy grail of #CADD: P-L binding #affinity prediction. By reframing limits of data & models, we can focus on the next solvable challenges - a sharp reminder of complexity & progress ahead.
#CECAM @cecamevents.bsky.social @iocbprague.bsky.social
#CECAM @cecamevents.bsky.social @iocbprague.bsky.social
Reposted by Radoslav Krivak
This afternoon at our @cecamevents.bsky.social Workshop in Prague:
Talks by Ulf Ryde, Ran Friedman & Charles-Alexandre Mattelaer explored QM methods for binding affinity, energy decomposition & binding geometries. Great discussions on rigorous QM in drug design!
#compchem @iocbprague.bsky.social
Talks by Ulf Ryde, Ran Friedman & Charles-Alexandre Mattelaer explored QM methods for binding affinity, energy decomposition & binding geometries. Great discussions on rigorous QM in drug design!
#compchem @iocbprague.bsky.social
September 9, 2025 at 9:35 PM
This afternoon at our @cecamevents.bsky.social Workshop in Prague:
Talks by Ulf Ryde, Ran Friedman & Charles-Alexandre Mattelaer explored QM methods for binding affinity, energy decomposition & binding geometries. Great discussions on rigorous QM in drug design!
#compchem @iocbprague.bsky.social
Talks by Ulf Ryde, Ran Friedman & Charles-Alexandre Mattelaer explored QM methods for binding affinity, energy decomposition & binding geometries. Great discussions on rigorous QM in drug design!
#compchem @iocbprague.bsky.social
Reposted by Radoslav Krivak
Morning session of our #CECAM Workshop in Prague featured @gdefabritiis.bsky.social presenting a ML force field for drug discovery, Julien Michel on electrostatic embedding for ML/MM free energy calcs, and Carlos Cruz Marin on ML models for logP.
@iocbprague.bsky.social @cecamevents.bsky.social
@iocbprague.bsky.social @cecamevents.bsky.social
September 9, 2025 at 9:32 PM
Morning session of our #CECAM Workshop in Prague featured @gdefabritiis.bsky.social presenting a ML force field for drug discovery, Julien Michel on electrostatic embedding for ML/MM free energy calcs, and Carlos Cruz Marin on ML models for logP.
@iocbprague.bsky.social @cecamevents.bsky.social
@iocbprague.bsky.social @cecamevents.bsky.social
Reposted by Radoslav Krivak
Closing Day2 with exciting talks:
M.Lepsik on #SQM scoring on AI-generated structures,M.Hennemann on local properties at P-L interfaces & I.Gordiy on enhanced sampling with ML potentials.Inspiring end before our social dinner!
@cecamevents.bsky.social @iocbprague.bsky.social @iocbtech.bsky.social
M.Lepsik on #SQM scoring on AI-generated structures,M.Hennemann on local properties at P-L interfaces & I.Gordiy on enhanced sampling with ML potentials.Inspiring end before our social dinner!
@cecamevents.bsky.social @iocbprague.bsky.social @iocbtech.bsky.social
September 9, 2025 at 9:47 PM
Closing Day2 with exciting talks:
M.Lepsik on #SQM scoring on AI-generated structures,M.Hennemann on local properties at P-L interfaces & I.Gordiy on enhanced sampling with ML potentials.Inspiring end before our social dinner!
@cecamevents.bsky.social @iocbprague.bsky.social @iocbtech.bsky.social
M.Lepsik on #SQM scoring on AI-generated structures,M.Hennemann on local properties at P-L interfaces & I.Gordiy on enhanced sampling with ML potentials.Inspiring end before our social dinner!
@cecamevents.bsky.social @iocbprague.bsky.social @iocbtech.bsky.social
Reposted by Radoslav Krivak
We opened Day 2 of our #CECAM flagship workshop in Prague with the CECAM director Andrea Cavalli, highlighting steered #MD, dynamical docking & the complexity of binding energetics, and the challenges ahead. 🚀
#CECAMinPrague @iocbprague.bsky.social @cecamevents.bsky.social @iocbtech.bsky.social
#CECAMinPrague @iocbprague.bsky.social @cecamevents.bsky.social @iocbtech.bsky.social
September 9, 2025 at 11:21 AM
We opened Day 2 of our #CECAM flagship workshop in Prague with the CECAM director Andrea Cavalli, highlighting steered #MD, dynamical docking & the complexity of binding energetics, and the challenges ahead. 🚀
#CECAMinPrague @iocbprague.bsky.social @cecamevents.bsky.social @iocbtech.bsky.social
#CECAMinPrague @iocbprague.bsky.social @cecamevents.bsky.social @iocbtech.bsky.social
Reposted by Radoslav Krivak
Day 1 of our #CECAM Flagship Workshop in Prague started strong!
Talks by Kennie Merz, Jan Řezáč, Markus Hermann & Hamza Ibrahim sparked great discussion on #QM, #ML & #DrugDesign
Thanks to @iocbprague.bsky.social, @iocbtech.bsky.social & @cecamevents.bsky.social for support!
#compchem #SQM
Talks by Kennie Merz, Jan Řezáč, Markus Hermann & Hamza Ibrahim sparked great discussion on #QM, #ML & #DrugDesign
Thanks to @iocbprague.bsky.social, @iocbtech.bsky.social & @cecamevents.bsky.social for support!
#compchem #SQM
September 8, 2025 at 12:06 PM
Day 1 of our #CECAM Flagship Workshop in Prague started strong!
Talks by Kennie Merz, Jan Řezáč, Markus Hermann & Hamza Ibrahim sparked great discussion on #QM, #ML & #DrugDesign
Thanks to @iocbprague.bsky.social, @iocbtech.bsky.social & @cecamevents.bsky.social for support!
#compchem #SQM
Talks by Kennie Merz, Jan Řezáč, Markus Hermann & Hamza Ibrahim sparked great discussion on #QM, #ML & #DrugDesign
Thanks to @iocbprague.bsky.social, @iocbtech.bsky.social & @cecamevents.bsky.social for support!
#compchem #SQM
Reposted by Radoslav Krivak
Tomorrow we kick off our #CECAM Flagship Workshop on Quantum Chemistry for Drug Design (Sept 8–10, Prague). 3 days of cutting-edge talks bridging #QM #ML & #drugdesign with world-class speakers shorturl.at/5sooU
#compchem #SQM @iocbtech.bsky.social @cecamevents.bsky.social @iocbprague.bsky.social
#compchem #SQM @iocbtech.bsky.social @cecamevents.bsky.social @iocbprague.bsky.social
September 7, 2025 at 10:18 AM
Tomorrow we kick off our #CECAM Flagship Workshop on Quantum Chemistry for Drug Design (Sept 8–10, Prague). 3 days of cutting-edge talks bridging #QM #ML & #drugdesign with world-class speakers shorturl.at/5sooU
#compchem #SQM @iocbtech.bsky.social @cecamevents.bsky.social @iocbprague.bsky.social
#compchem #SQM @iocbtech.bsky.social @cecamevents.bsky.social @iocbprague.bsky.social
Reposted by Radoslav Krivak
CATH turns 30 years old 🥳
They celebrate with a Symposium on September 16th! I'll be presenting our work: "An Atlas of Energetic Evolutionary Constraints Across Protein Families"
Unbelievable selection of speakers! So if you are around London, you can register to attend:
tinyurl.com/2pnk8hj5
They celebrate with a Symposium on September 16th! I'll be presenting our work: "An Atlas of Energetic Evolutionary Constraints Across Protein Families"
Unbelievable selection of speakers! So if you are around London, you can register to attend:
tinyurl.com/2pnk8hj5
August 23, 2025 at 3:08 PM
CATH turns 30 years old 🥳
They celebrate with a Symposium on September 16th! I'll be presenting our work: "An Atlas of Energetic Evolutionary Constraints Across Protein Families"
Unbelievable selection of speakers! So if you are around London, you can register to attend:
tinyurl.com/2pnk8hj5
They celebrate with a Symposium on September 16th! I'll be presenting our work: "An Atlas of Energetic Evolutionary Constraints Across Protein Families"
Unbelievable selection of speakers! So if you are around London, you can register to attend:
tinyurl.com/2pnk8hj5
Reposted by Radoslav Krivak
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...
😂
Look what they did to Notepad. Shut the fuck up. This is Notepad. You are not welcome here. Oh yeah "Let me use Copilot for Notepad". "I'm going to sign into my account for Notepad". What the fuck are you talking about. It's Notepad.
August 27, 2025 at 10:59 AM
😂
Reposted by Radoslav Krivak
The first day of our bioML symposium at @iocbprague.bsky.social went very well. It is amazing to see how fast this field is moving forward. Thanks to everyone for the fantastic talks! 🤖🧬
August 21, 2025 at 8:22 PM
The first day of our bioML symposium at @iocbprague.bsky.social went very well. It is amazing to see how fast this field is moving forward. Thanks to everyone for the fantastic talks! 🤖🧬
Reposted by Radoslav Krivak
Our significantly expanded preprint is out. In it we show that pancreatic cancer cells can transfer ribosomes via tunnelling nanotubes and rescue protein synthesis when co-cultured with cells with impaired ribosomal biogenesis.
🧪
(Includes some #bayesian #rstats inspired by @rmcelreath.bsky.social)
🧪
(Includes some #bayesian #rstats inspired by @rmcelreath.bsky.social)
Ribosome transfer via tunnelling nanotubes rescues protein synthesis in pancreatic cancer cells
Background: Pancreatic ductal adenocarcinoma (PDAC) is considered as one of the deadliest types of cancer. Tunnelling nanotubes (TNTs) are thin, membranous, intercellular communication structures obse...
www.biorxiv.org
August 6, 2025 at 7:56 AM
Our significantly expanded preprint is out. In it we show that pancreatic cancer cells can transfer ribosomes via tunnelling nanotubes and rescue protein synthesis when co-cultured with cells with impaired ribosomal biogenesis.
🧪
(Includes some #bayesian #rstats inspired by @rmcelreath.bsky.social)
🧪
(Includes some #bayesian #rstats inspired by @rmcelreath.bsky.social)
Reposted by Radoslav Krivak
New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...
patwalters.github.io/Three-Papers...
July 22, 2025 at 1:40 PM
New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...
patwalters.github.io/Three-Papers...
Reposted by Radoslav Krivak
![Travis Kalanick, the founder of Uber who no longer works at the company, appeared on All-In to talk with hosts Jason Calacanis and Chamath Palihapitiya about the future of technology. When the topic turned to AI, Kalanick discussed how he uses xAI’s Grok, which went haywire last week, praising Adolf Hitler and advocating for a second Holocaust against Jews.
“I’ll go down this thread with [Chat]GPT or Grok and I’ll start to get to the edge of what’s known in quantum physics and then I’m doing the equivalent of vibe coding, except it’s vibe physics,” Kalanick explained. “And we’re approaching what’s known. And I’m trying to poke and see if there’s breakthroughs to be had. And I’ve gotten pretty damn close to some interesting breakthroughs just doing that.”](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:qlnirjwff4ibiw3wchmleszo/bafkreiac2szurc5dnw6klquhpjmo7iafg4n6fwmrqyred7jrrph6h6mptq@jpeg)
July 16, 2025 at 1:28 AM
😂
July 14, 2025 at 1:03 PM
😂
Reposted by Radoslav Krivak
🎉 I am thrilled to share that our latest work on is now publicly available on @biorxivpreprint.bsky.social.
The title is "Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish ints interaction with the Ser/Thr kinase CK1α".
🔗 Pre-print: www.biorxiv.org/content/10.1...
The title is "Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish ints interaction with the Ser/Thr kinase CK1α".
🔗 Pre-print: www.biorxiv.org/content/10.1...
July 1, 2025 at 1:51 PM
🎉 I am thrilled to share that our latest work on is now publicly available on @biorxivpreprint.bsky.social.
The title is "Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish ints interaction with the Ser/Thr kinase CK1α".
🔗 Pre-print: www.biorxiv.org/content/10.1...
The title is "Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish ints interaction with the Ser/Thr kinase CK1α".
🔗 Pre-print: www.biorxiv.org/content/10.1...
Reposted by Radoslav Krivak
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...