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Karel "CaCO3" Berka

@krapnik.bsky.social
2K followers 4.8K following 659 posts

theoretical physical chemist, molecular modeller and chem- and bioinformatician - #AlphaFoldology enthusiast Palacky University Olomouc, ORCID:0000-0001-9472-2589 #boardgamegeek (tweets my own) #ELIXIRCZ

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Karel "CaCO3" Berka @krapnik.bsky.social · 17/08/2026
O víkendu jsem si chtěl vyzkoušet napsat aplikaci na trošku jiný typ výzkumu, než je u chemika obvyklé, a tak jsem přichystal Trestní dilemata. Princip je jednoduchý - dostanete na výběr mezi dvěma delikty a musíte si vybrat, který je podle Vás závažnější. media.giphy.com/media/v1.Y2l...
giphy.com
Weighing Seth Meyers GIF by Late Night with Seth Meyers - Find & Share on GIPHY
GIPHY image by Late Night with Seth Meyers
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Karel "CaCO3" Berka @krapnik.bsky.social · 26/07/2026
Sad news to #CompChem Pavel Jungwirth passed away… www.uochb.cz/en/news/811/...
uochb.cz
Pavel Jungwirth, a leading figure in the world of chemistry, has died
The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences is deeply saddened to announce that on Thursday 23 July 2026, our outstanding colleague, teacher, mentor and…
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Karel "CaCO3" Berka @krapnik.bsky.social · 30/06/2026
If you want to play some biochemical boardgame on summer holidays - you can try my AA-Dobble - karelberka.github.io/amino-acid-d... #proteins #chemsky
karelberka.github.io
AA-Dobble: Biogenní aminokyseliny
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 27/06/2026
Part 2 may be of most use to experienced users of AlphaFold and related programs. It covers the origin of the AF scores in benchmarking protein structure prediction (GDT-TS, LDDT, TM score) and the AF versions of these scores (pLDDT, PAE, ipTM, ipSAE, LIS). www.youtube.com/watch?v=WW_X...
youtube.com
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 27/06/2026
I gave a workshop on AlphaFold & related programs @ the University of Utah. Part 1 covers protein structure prediction before/after AlphaFold & deep learning neural networks. Part 2 covers the math behind the scores. Part 3 covers PyMOL & the webservers. youtube.com/@rolanddunbr...
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Karel "CaCO3" Berka @krapnik.bsky.social · 25/06/2026
Antigravity (or other agentic AI who wrote code) is cool tool for making science edu apps for computational chemistry. For instance, I vibecoded this interactive atomic orbital simulator this afternoon based on discussion with student… karelberka.github.io/orbital-simu... (it is in Czech now)
karelberka.github.io
3D Simulátor Atomových Orbitalů
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Karel "CaCO3" Berka @krapnik.bsky.social · 15/06/2026
nice #alphafoldology gym for alternative structure prediction
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Stephanie Wankowicz @stephanieaw.bsky.social · 15/06/2026
sampleworks allows you to hold the experimental loss fixed and benchmark structure predictors head-to-head, or freeze the model and sweep guidance methods + hyperparameters. github.com/diff-use/sam...
github.com
GitHub - diff-use/sampleworks: Framework for modified sampling from biomolecular generative models
Framework for modified sampling from biomolecular generative models - diff-use/sampleworks
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Iona Brand @mikeiona.bsky.social · 07/06/2026
Did you ever see the "Not The Nine O'Clock News" sketch? m.youtube.com/watch?v=asUy...
m.youtube.com
Not the Nine O'Clock News - Monty Pythons worshipers
YouTube video by ZuzuzuLooker
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Karel "CaCO3" Berka @krapnik.bsky.social · 04/06/2026
another #alphafoldology tool - DeltaDiff - for prediction of mutant protein structures.
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Karel "CaCO3" Berka @krapnik.bsky.social · 04/06/2026
pipeline for #alphafoldology pipeline for identification of PPIs
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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 03/06/2026
🧬 Claude isn't the only AI that can query PDBe. PDBe MCP Servers work with other AI clients too, such as Google Antigravity. You only need one protocol for any MCP-compatible AI. 🎥 Watch the install walkthrough 👇 📦 github.com/PDBeurope/PDBe-MCP-Servers #PDBe #MCP #GoogleAntigravity #AI
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Karel "CaCO3" Berka @krapnik.bsky.social · 11/05/2026
Power of Boron lecture by Michael Londesborough from IIC AV CR at @fchupol.bsky.social www.youtube.com/live/j3PvXHe... #chemsky
youtube.com
Michael Londesborough - Boron Power
YouTube video by Katedra fyzikální chemie UPOL
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Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Sebastian Hiller on integrative NMR #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Andrea Soranno on IDP biophysics #ppps2026
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Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Ahrum Son on protein structural changes in alzheimer’s disease #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 07/05/2026
And great opening of Prague Protein Spring by David Baker @nd-bakerlab.bsky.social #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 07/05/2026
Next speaker is Michele Vendruscolo on dugging undruggable #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
Eugene Shakhnovich on chaperonines helping bacteia to resist antibiotics #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
Patricia Clark on silent mutations and protein folding #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
On neurodegeneration by Nikolay Dokholyan #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
Alena Khmelinskaia @akhmelinlab.bsky.social promoting @rosettacommons.bsky.social -Con after her amazing talk on design of protein nanostructures #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
Sameer Velankar @pdbeurope.bsky.social @ebi.embl.org ready to his talk on AI in biology #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
Gennady Verkhivker on AI and allostery in protein kinases #pps2026
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Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Basile Wicky @ethz.ch on protein design #pps2026
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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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Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Agnes Toth-Petroczy @tothpetroczylab.bsky.social on IDPs #pps2026
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 07/05/2026
New Syntax for PDB DOIs for Entries Released After July 21, 2027 PDB entries deposited after July 20, 2027 will only be assigned extended PDB IDs and will follow a new DOI syntax.
rcsb.org
New Syntax for PDB DOIs for Entries Released After July 21, 2027
PDB entries deposited after July 20, 2027 will only be assigned extended PDB IDs and will follow a new DOI syntax.
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macomix @macomix.bsky.social · 05/05/2026
Babička je do neděle v aukci. Držte palce, nebo si ji radši vydražte ;) www.obrazyvaukci.cz/polozka/maco...
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тoмáš víт 🌌 @tomulinek.bsky.social · 04/05/2026
Originální řešení pro velkoobjemový #3Dtisk vzniká i v Česku. Byl jsem se podívat za Jiřím Samkem v Hradci Králové na velkého robota, který umí připravovat obrovské výtisky z termoplastů. A tím „obrovské“ myslím v řádu mnoha metrů a mnoha tun. Mikroreportáž: www.linkedin.com/posts/tomvit...
linkedin.com
#3dtisk #sinumerik #sinucraft #lfam #aditivnivyroba #prumysl #vyroba | Tomas Vit
Originální řešení pro velkoobjemový #3Dtisk vzniká i v Česku Ve čtvrtek jsem se byl podívat za Jiřím Samkem v Hradci Králové na velkého robota, který umí připravovat obrovské výtisky z termoplastů. ...
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Simon Fisher @profsimonfisher.bsky.social · 03/05/2026
Been training for this moment my whole life.
A 3x3 CAPTCHA grid showing different stock images of DNA, several of which have unusual left-handed double-helices, rather than the right-handed structure most typically seen in nature. To prove that the user is not a robot, they simply need to click on "all DNA stock images with messed-up chirality".
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Karel "CaCO3" Berka @krapnik.bsky.social · 29/04/2026
Olomouc na Zemi, Zeměkoule na AFO v Olomouci
Olomouc na Zemi, Zeměkoule na AFO v Olomouci
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Karel "CaCO3" Berka @krapnik.bsky.social · 29/04/2026
na AFO jsem si zaridil Marsovsky rover, hec @chmee2.bsky.social
ovladani vozitka na Marsu
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Karel "CaCO3" Berka @krapnik.bsky.social · 28/04/2026
Artistic beauty of protein structures by @irinabezsonova.bsky.social
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Karel "CaCO3" Berka @krapnik.bsky.social · 23/04/2026
2nd Czech PhD bioinformatics conference started in Křelov near Olomouc with the Abdulrahman Kahraman from NW university Basel about how to hit cancer hard with bioinformatics and precision oncology 🧬💊🖥️
Abdulman Kahraman invited lecture on hitting Cancer hard with bioinformatics/data science in Precision Oncologywith specific focus on the alternating slicing variants
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Chemistry World @chemistryworld.com · 22/04/2026
Battery week 2026 is coming up and in partnership with The Faraday Institution, we’ll be hosting a series of free webinars. Register to join us & hear about the future of battery power: @faradaydiscussions.rsc.org @rsc.org #ChemSky #Batteries www.chemistryworld.com/collections/...
chemistryworld.com
Energy storage and batteries | Chemistry World
In this collection, we explore energy storage and battery research, covering innovative battery chemistries, materials design, device fabrication techniques, solutions to transition to clean energy, a...
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Vittorio Saggiomo @vsaggiomo.bsky.social · 05/04/2026
Happy Easter people :)
Happy Ester
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Karel "CaCO3" Berka @krapnik.bsky.social · 27/03/2026
Do you know, how to get two undisturbed hours for work? Put into calendar both alternating time slots for a meeting at rectorate and then miss the update that the one in two weeks was selected. For more tips on academic time scheduling - do not follow me. ;)
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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 26/03/2026
𝗣𝗗𝗕𝗲 𝗘𝗻𝘁𝗿𝘆 𝗣𝗮𝗴𝗲𝘀 just got better! 🚀 🔹 New tab with links to partner and related databases 🔹 PDBe extended codes now displayed 🔹 More data fields requested by the community Explore an entry: pdbe.org/12ca We need your feedback! More updates are coming!
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Karel "CaCO3" Berka @krapnik.bsky.social · 24/03/2026
grant submission feeling in the air…
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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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Dr. Petr Brož @chmee2.bsky.social · 03/03/2026
A je to. V neděli večer jsem odevzdal rukopis třetího dílu naši knižní série #Vesmírníček aneb usínáme s vědou. Tentokrát se vrátíme zpátky na Zemi a poodhalíme si taje geologie a vysvětlíme si, proč naše rodná hrouda vypadá, jak vypadá a co ji ještě čeká. Vyjde podzim 2026!
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Karel "CaCO3" Berka @krapnik.bsky.social · 02/03/2026
97h #3Dprint Guess protein ;)
Mtb ATPsynthaseMtb ATP synthase
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📚Martin Šinkovský📖🖋 @masinko.czesky.online · 02/03/2026
A máme tu nejoblíbenější disciplínu ze všech nejoblíbenějších disciplín. HLASOVÁNÍ! Temné obilí se dostalo do finále Cen Olomouckého kraje za kultůru. Je mi jasné, že takový Festival vojenských kuchyní nemáme šanci porazit, ale i tak, když utrousíte hlas a pošlete to dál, budu rád. Díky moc... Pa
cenykraje.cz
Ceny Olomouckého kraje
Vážení příznivci turistiky a cestování, dopad epidemie koronaviru na cestovní ruch je mimořádně tvrdý. To je třeba říci na rovinu a nepřivírat před tím oči.
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Karel "CaCO3" Berka @krapnik.bsky.social · 19/02/2026
Bylo fajn vyhrat jedno kolo v univezitnim AZ kvizu vedeckych popularizatoru… ;)
winning 1.round of UP AZ-kviz
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Karel "CaCO3" Berka @krapnik.bsky.social · 17/02/2026
Dobré to včera bylo…
Dan Přibáň speaking about a journey to Mongolia with yellow frogs Végu a Vóža
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 11/02/2026
Adopt early: New PDB Beta Archive Available for Testing The beta archive supports and is organized around the extended PDB ID transition The directory structure **will replace the current PDB Archive** when all 4-character PDB IDs are assigned Details:
rcsb.org
New PDB Beta Archive Available for Testing
The beta archive is organized around and in support of the transition to extended PDB IDs. The directory structure will replace the current PDB Archive when all 4-character PDB IDs have been assigned.
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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 26/01/2026
We're hiring a 𝐓𝐫𝐚𝐢𝐧𝐢𝐧𝐠 𝐒𝐩𝐞𝐜𝐢𝐚𝐥𝐢𝐬𝐭 for 𝐀𝐥𝐩𝐡𝐚𝐅𝐨𝐥𝐝 𝐃𝐚𝐭𝐚𝐛𝐚𝐬𝐞 (AFDB)! Join our team to develop training content, create workshops, and drive global engagement with AlphaFold and AFDB. Full-time, hybrid role. Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d... #AFDB #Jobs #emblebi
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Karel "CaCO3" Berka @krapnik.bsky.social · 26/01/2026
Our 9th Advanced in silico Drug Design workshop just started - you can watch #9ADD at www.youtube.com/playlist?lis... All materials will be available 9ADD workshop webpage> www.kfc.upol.cz/9add together with program #compchemsky #chemsky #medchemsky 💊🧬🖥️
youtube.com
9ADD - 9th Advanced Drug Design workshop 2026 - YouTube
9ADD workshop https://www.kfc.upol.cz/9add January 26, 2026 – January 30, 2026 Palacky University OlomoucThe 9ADD workshop focuses on using in silico tools a...
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Brendan @chemscrapes.bsky.social · 23/01/2026
For this weekend only and only pushing on bluesky :)...get both chemscrapess book (PDF download) at 25% off when purchased together. #chemchat #chemsky
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