Radoslav Krivak

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)

Play a game of Go against an old-fashioned AI, and watch as it thinks! The curves visualize spheres of influence for each potential future position it considers. Try it at www.bewitched.com/go

guys I just tried googling this to find the exact Andor quote and jesus fucking christ guys what the fuck is happening here

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. https://loom.ly/gZY5ylY #StructuralBiology #Biophysics #OpenScience #AI

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

Tomas Pluskal @pluskal-lab.org on plants, their products and AI #pps2026

Now published in NSMB! Paper: doi.org/10.1038/s415... Full PDF: rdcu.be/fhBtI Overview of additions since the preprint👇 (1/5)

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:

FT comments section this morning - saying what everyone else is thinking, right?

PDB Reaches a New Milestone: more than 250,000 entries

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... 🧵👇

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!

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

today #3Dprint protein is ferritin (PDB: 6I36) available here: www.printables.com/model/141627...

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 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

YouTube link for MLCB2025 is up! Starting in 30 min. www.youtube.com/live/19I7xTh...

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

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

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

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

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

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

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

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

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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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! 🤖🧬

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)

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

My god these guys are such spectacular morons gizmodo.com/billionaires...

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🎉 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...

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...

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.

🚀 GPU-accelerated docking to P2Rank-predicted pockets

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...

🚀 GPU-accelerated docking to P2Rank-predicted pockets

Scientific institutions have a long history of anticipatory obedience www.chemistryworld.com/opinion/scie...

🚀 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

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

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?! 😍

“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.

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

Congratulations! 🎉