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Radoslav Krivak

@rdkbio.bsky.social
3K followers 4K following 152 posts

🧬 Structural Bioinformatics | 💊 AI/ML for Drug Discovery | Geometric DL 🔬 @iocbprague.bsky.social, prev. PhD @cusbg.bsky.social @mff.unikarlova.cuni.cz

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Reposted by Radoslav Krivak
Jonn Elledge @jonnelledge.bsky.social · 28/05/2026
guys I just tried googling this to find the exact Andor quote and jesus fucking christ guys what the fuck is happening here
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OpenBind @openbind.bsky.social · 13/05/2026
Our latest blog walks through how the affinity and kinetics data in the EV‑A71 2A OpenBind release were produced - from target selection to large‑scale structure and binding measurements. loom.ly/gZY5ylY #StructuralBiology #Biophysics #OpenScience #AI
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IOCB Tech @iocbtech.bsky.social · 21/05/2026
Czech biotech stands on stronger foundations than many still assume. Nearly 430 entities, CZK 97.5bn in annual revenue, and growing investor attention show real momentum. But further growth will depend on one thing: turning strong science into investable, scalable projects. #Biotech #Czechia
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Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Tomas Pluskal @pluskal-lab.org on plants, their products and AI #pps2026
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Elixir of Progress @elucidating.extradimensional.space · 13/04/2026
This article is wild. The asteroid Bennu contains enough amino acid variety to construct a metabolism. A highly limited amino acid library from asteroid Bennu yields wide-ranging protein folds | Nature Communications
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A highly limited amino acid library from asteroid Bennu yields wide-ranging protein folds - Nature Communications
The origins of life are steeped in mystery, but the AI revolution could transform this field. Here, the authors use AI-based protein design software to uncover a broad range of protein folds that can be formed from small, primordial amino acid libraries constrained by asteroid and prebiotic chemistry data.
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Peter Škrinjar @peterskrinjar.bsky.social · 11/05/2026
Now published in NSMB! Paper: doi.org/10.1038/s415... Full PDF: rdcu.be/fhBtI Overview of additions since the preprint👇 (1/5)
doi.org
Evaluating generalization in protein–ligand cofolding methods - Nature Structural & Molecular Biology
This work introduces the Runs N’ Poses dataset for benchmarking deep learning methods on the protein–ligand complex prediction task. It shows that current methods rely on memorization, challenging the...
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Reposted by Radoslav Krivak
Andreas Kirsch @blackhc.bsky.social · 18/03/2026
A while back, Andrej Karpathy said the app store will be replaced by generated, disposable software," and Amjad Masad predicted that the value of all application software will go to zero I think this "ephemeral software hypothesis" is wrong, though, and I want to explain why:
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Neil Lewis @neil-lewis.bsky.social · 05/03/2026
FT comments section this morning - saying what everyone else is thinking, right?
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 05/03/2026
PDB Reaches a New Milestone: more than 250,000 entries
rcsb.org
PDB Reaches a New Milestone
The PDB now contains more than 250,000 entries
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Reposted by Radoslav Krivak
Anton Bushuiev @anton-bushuiev.bsky.social · 05/03/2026
ProteinTTT is now easy to run on Hugging Face Spaces and Google Colab. We’ll also be presenting the paper at ICLR 2026 🇧🇷 🤗 Hugging Face Space: huggingface.co/spaces/pimen... ⚙️ Google Colab: colab.research.google.com/drive/1l_h7c... 🧵👇
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Anton Bushuiev @anton-bushuiev.bsky.social · 27/10/2025
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!
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Anton Bushuiev @anton-bushuiev.bsky.social · 23/10/2025
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/🧵
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Radoslav Krivak @rdkbio.bsky.social · 25/09/2025
Finally, Mol* with a human face
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Karel "CaCO3" Berka @krapnik.bsky.social · 16/09/2025
today #3Dprint protein is ferritin (PDB: 6I36) available here: www.printables.com/model/141627...
ferritin 3d modelferritin 3d model open
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Tomáš Pluskal @pluskal-lab.org · 16/09/2025
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.
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Charles University, Faculty of Science @sciencecharles.bsky.social · 16/09/2025
🌿 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
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Radoslav Krivak @rdkbio.bsky.social · 14/09/2025
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?
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David A Knowles @davidaknowles.bsky.social · 10/09/2025
YouTube link for MLCB2025 is up! Starting in 30 min. www.youtube.com/live/19I7xTh...
youtube.com
Machine Learning in Computational Biology 2025
YouTube video by Machine Learning in Computational Biology
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Adam Pecina @adampecina.bsky.social · 10/09/2025
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
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Adam Pecina @adampecina.bsky.social · 09/09/2025
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
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Adam Pecina @adampecina.bsky.social · 09/09/2025
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
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Adam Pecina @adampecina.bsky.social · 09/09/2025
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
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Adam Pecina @adampecina.bsky.social · 09/09/2025
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
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Adam Pecina @adampecina.bsky.social · 08/09/2025
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
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Adam Pecina @adampecina.bsky.social · 07/09/2025
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
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Gonzalo Parra @gonzaparra.bsky.social · 23/08/2025
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
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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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Radoslav Krivak @rdkbio.bsky.social · 27/08/2025
😂
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Tomáš Pluskal @pluskal-lab.org · 21/08/2025
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! 🤖🧬
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Jan Trnka @jantrnka.bsky.social · 06/08/2025
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)
biorxiv.org
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...
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Pat Walters @wpwalters.bsky.social · 22/07/2025
New Practical Cheminformatics Post patwalters.github.io/Three-Papers...
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Paul Waldman @paulwaldman.bsky.social · 16/07/2025
My god these guys are such spectacular morons gizmodo.com/billionaires...
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.”
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Radoslav Krivak @rdkbio.bsky.social · 14/07/2025
😂
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Dr Javier Sánchez Utgés @javierutges.bsky.social · 01/07/2025
🎉 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...
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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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Bob Čáp 🇵🇸🇺🇦 @bobcap.cz · 23/06/2025
Všem, kteří hájí či podporují ilegální útoky Izraele a USA na Írán s tím, že jde o útok na nenáviděný režim, jehož pád místní uvítají: Představte si, že je rok 1988 a USA na obyvatele ČSSR shazují bomby, aby jim pomohli od komunistů. To by bylo radosti v ulicích.
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Radoslav Krivak @rdkbio.bsky.social · 27/06/2025
🚀 GPU-accelerated docking to P2Rank-predicted pockets
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 26/06/2025
This is cool. An archaeal species with no metabolic genes. Just replicative genes (ribosomes, messenger and transfer RNAs). 238kb genome. www.biorxiv.org/content/10.1...
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Radoslav Krivak @rdkbio.bsky.social · 27/06/2025
🚀 GPU-accelerated docking to P2Rank-predicted pockets
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Ellen Moons @solellen.bsky.social · 25/06/2025
Scientific institutions have a long history of anticipatory obedience www.chemistryworld.com/opinion/scie...
chemistryworld.com
Scientific institutions have a long history of anticipatory obedience
Societies should learn from this and speak up to support inclusion
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Radoslav Krivak @rdkbio.bsky.social · 10/06/2025
🚀 Our paper on the updated PrankWeb, a web app for protein binding site prediction using P2Rank, is out in @narjournal.bsky.social. Now with docking integration! 👨‍💻 Try it: prankweb.cz 📄 Paper: doi.org/10.1093/nar/... 💻 GitHub: github.com/cusbg/prankweb Developed at @cusbg.bsky.social
Screenshot of PrankWeb.
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Marian Novotny @majek.bsky.social · 19/06/2025
Fantastic to work with so many talented people! today at departmental conference of cell biology department of @sciencecharles.bsky.social . Many thanks to our guests from Israel for joining us and sharing their results and time with us
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Radoslav Krivak @rdkbio.bsky.social · 19/06/2025
Claude Code
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Martin Lulak @polarandycz.bsky.social · 18/06/2025
Not only the Prague planetarium have the most modern LED projection in the world. They also do have these awesome mirrors on toilets! How cool is that?! 😍
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Derek Lowe @dereklowe.bsky.social · 17/06/2025
“What is common knowledge in your field, but shocks outsiders?” Most drugs have several activities in the human body, and discovery of these effects goes on for years after they are on the market.
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Philip Ball @philipcball.bsky.social · 17/06/2025
Beyond that though, I have been doing this sci comm stuff for a long time, and I have NEVER before known a time when I've had to grapple with so many nonsensical claims from tech leaders. There's just a constant stream, which most of the media gobbles up. I'm frankly really tired of it. 9/9
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Charles University Structural Bioinformatics Group @cusbg.bsky.social · 16/06/2025
Congratulations! 🎉
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Radoslav Krivak @rdkbio.bsky.social · 10/06/2025
🚀 Our paper on the updated PrankWeb, a web app for protein binding site prediction using P2Rank, is out in @narjournal.bsky.social. Now with docking integration! 👨‍💻 Try it: prankweb.cz 📄 Paper: doi.org/10.1093/nar/... 💻 GitHub: github.com/cusbg/prankweb Developed at @cusbg.bsky.social
Screenshot of PrankWeb.
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Roman Bushuiev @roman-bushuiev.bsky.social · 26/05/2025
Mass spectrometry is a key method to discover and identify molecules in biological and environmental samples. Yet, >90% of mass spectra remain hard to interpret. In our recent paper, we present DreaMS — a foundation model to interpret mass spectra of small molecules. www.nature.com/articles/s41...
nature.com
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - Nature Biotechnology
A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra.
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IOCB Prague @iocbprague.bsky.social · 28/05/2025
⚛️ @pluskal-lab.org from IOCB Prague, together with his student @roman-bushuiev.bsky.social and colleagues from #CIIRC CTU, Josef Šivic and @anton-bushuiev.bsky.social, have developed a machine learning model called #DreaMS – which accelerates the analysis of previously unknown molecules.
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