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Radoslav Krivak

@rdkbio.bsky.social

2.8K followers 3.7K following 150 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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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)

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Radoslav Krivak @rdkbio.bsky.social · 11d

The link here doesn't seem to work...

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Radoslav Krivak @rdkbio.bsky.social · 12d

Every limitation of AlphaFold2/structure prediction you noted also applies to co-folding tools, but even more so.

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Radoslav Krivak @rdkbio.bsky.social · 14d

Finally, Mol* with a human face

RCSB Protein Data Bank @rcsbpdb.bsky.social · 14d

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

Radoslav Krivak @rdkbio.bsky.social · 21d

Curious how China comes into play here. Is it mainly about market opportunities, competition, or something else?

Radoslav Krivak @rdkbio.bsky.social · 22d

Yes... I wish Bluesky was that, but this is where we are. Linked has this recycling thing when it shows you 4 week old posts if they are relevant which is actually good.

Reposted by Radoslav Krivak

Karel "CaCO3" Berka @krapnik.bsky.social · 22d

today #3Dprint protein is ferritin (PDB: 6I36)

available here:
www.printables.com/model/141627...

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Reposted by Radoslav Krivak

Tomáš Pluskal @pluskal-lab.org · 23d

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.

IOCB Prague @iocbprague.bsky.social · 23d

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

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Reposted by Radoslav Krivak

Charles University, Faculty of Science @sciencecharles.bsky.social · 23d

🌿 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 · 24d

@asarigun.bsky.social

Radoslav Krivak @rdkbio.bsky.social · 24d

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?

Matthieu da Costa @mdc-biocat.bsky.social · Aug 31

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)

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Reposted by Radoslav Krivak

David A Knowles @davidaknowles.bsky.social · 28d

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

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Reposted by Radoslav Krivak

Adam Pecina @adampecina.bsky.social · 28d

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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Reposted by Radoslav Krivak

Adam Pecina @adampecina.bsky.social · 29d

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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Reposted by Radoslav Krivak

Adam Pecina @adampecina.bsky.social · 29d

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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Reposted by Radoslav Krivak

Adam Pecina @adampecina.bsky.social · 29d

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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Reposted by Radoslav Krivak

Adam Pecina @adampecina.bsky.social · 29d

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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Reposted by Radoslav Krivak

Adam Pecina @adampecina.bsky.social · Sep 8

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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Reposted by Radoslav Krivak

Adam Pecina @adampecina.bsky.social · Sep 7

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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Reposted by Radoslav Krivak

Gonzalo Parra @gonzaparra.bsky.social · Aug 23

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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Reposted by Radoslav Krivak

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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Radoslav Krivak @rdkbio.bsky.social · Aug 27

😂

Iain @iainnd.bsky.social · Aug 27

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.

Windows Notepad, the native simple text editor, now has formatting options and a Copilot button.

Reposted by Radoslav Krivak

Tomáš Pluskal @pluskal-lab.org · Aug 21

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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Reposted by Radoslav Krivak

Jan Trnka @jantrnka.bsky.social · Aug 6

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)

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

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Reposted by Radoslav Krivak

Pat Walters @wpwalters.bsky.social · Jul 22

New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...

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Reposted by Radoslav Krivak

Paul Waldman @paulwaldman.bsky.social · Jul 16

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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