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

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?

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...

😂

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...

😂

🎉 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

Claude Code

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! 🎉

🚀 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

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...

⚛️ @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.

I am #exhilarated to share that our new paper "LIGYSIS-web: a resource for the analysis of protein-ligand binding sites" is now published in @narjournal.bsky.social! After almost two years of development and more than 600 commits, LIGYSIS-web is out! 📜 : tinyurl.com/utges-LIGYSI...

Join us for the next #Bioinformatics seminar hosted by @sciencecharles.bsky.social and @mff.unikarlova.cuni.cz. Nora Martin from CRG : “How does the structure of a genotype-phenotype map shape variation and evolutionary processes?”. 📅 Wed, Apr 30 🕕 17:20 bioinformatics.cuni.cz/seminar

#Jalview goes the extra mile! Remember the integration with @chimerax.ucsf.edu or #PyMOL? Well, you can use these viewers to inspect #AlphaFold confidence scores #pLDDT and #PAE in multiple #sequence alignment and #structure! Multiple structure prediction confidence analysis made easy with Jalview!

Down into the details of how compounds and binding sites interact:

#research #proteindynamics #biophysics Unraveling the Tether: Exploring Representative Protein Linkers and Their Structural and Thermodynamical Properties (Šulc, Vondrášek) – JPhysChem B: doi.org/10.1021/acs.... @iocbprague.bsky.social @czechacademy.bsky.social @sciencecharles.bsky.social

Happy world homeopathy day

Back in July 2023 we organized a small bioML symposium at @iocbprague.bsky.social, and it turned out to be a very pleasant and successful event. This summer we are following up with a great line-up of speakers. Please register for free, deadline May 30. tinyurl.com/bioMLPrague25

3DSIG has now joined BlueSky!! Follow us there to keep building a strong community around the fields of Structural Bioinformatics and Computational Biophysics!

New release for #ipymolstar: I've added a widget for the amazing and very powerful MolViewSpec. This allows you to control the camera📷from python🐍, as well as all other molviewspec features 🎉 ipymolstar repo: github.com/jhsmit/ipymo... Molviewspec: molstar.org/mol-view-spec/

We are getting so many great abstracts!! This year's programme will look fabulous! You can still be part of it!! There is still one more week to go to send your work to this year's 3DSIG!! Do not miss the chance!!! Submit now! t.co/gCPpDtpzD8

🧪🇨🇿 A reminder: there’s a starter pack with Czech science institutions and research labs. A bunch of new ones have joined Bluesky lately -- and some, like Charles University (@charlesuni.cuni.cz), have fully made the move here from the other place.

🎙 Některé kroky Trumpova kabinetu se jeví absurdní, dopady na vědeckou komunitu i veřejné zdraví můžou být ale nebezpečné pro všechny. #podcast #chemic #iocb #uochb #scientist #vedec #iocb #uochb #iocbprague #akademievedcr www.uochb.cz/cs/novinky/6...