Sign in

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

PostsRepliesMedia
Karel "CaCO3" Berka @krapnik.bsky.social · 17/08/2026
Nicméně, nezapomínejte na to, že tresty mají své rozsahy a také se u trestání výrazně přihlíží k trestní historii pachatelů a recidivisté mají typicky tvrdší tresty. Oproti tomu tahle aplikace Vás staví do pozice porovnávání právnického "sférického kuřete ve vakuu".
000
Karel "CaCO3" Berka @krapnik.bsky.social · 17/08/2026
A aplikace karelberka.github.io/trestni-dile... pak na pozadí tyto hlasy sesbírá... (k ovládání stačí šipky a mezerník)
karelberka.github.io
Trestní Dilemata ČR | Srovnávač trestných činů a soudní praxe
Interaktivní srovnávač závažnosti trestných činů v ČR podle trestního zákoníku a reálné soudní praxe. Otestujte svůj právní a etický úsudek.
100
Karel "CaCO3" Berka @krapnik.bsky.social · 17/08/2026
Vaši volbu pak můžete srovnat s trestním zákoníkem a s webem jaktrestame.cz od Jakuba Drápala, Kláry Svitakové, Michala Šoltése a Jana Cibulky. A pak si můžete vybrat další náhodnou dvojici a další…
jaktrestame.cz
JakTrestame.cz
Zajímá vás, jaké tresty v České republice ukládáme? Ať už jde o profesní nebo osobní důvody, neexistuje místo, kde byste se dozvěděli více o tom, jak trestáme. Vedle statistik o uložených trestech zde...
100
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
100
Karel "CaCO3" Berka @krapnik.bsky.social · 14/08/2026
All the Mankind was good as well (as an inofficial prequel to Expanse)
010
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…
6153
Karel "CaCO3" Berka @krapnik.bsky.social · 19/07/2026
there is no secondary contact with membrane… just one TM-helix
GHR model from AF3 with OLA to model membrane
010
Karel "CaCO3" Berka @krapnik.bsky.social · 08/07/2026
ehm, v cem?
200
Karel "CaCO3" Berka @krapnik.bsky.social · 08/07/2026
beware - once you start reading it, you might have problem to stop…
000
Karel "CaCO3" Berka @krapnik.bsky.social · 03/07/2026
which series?
100
Karel "CaCO3" Berka @krapnik.bsky.social · 30/06/2026
added feature to show MO-LCAO combination on the fly…
000
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
010
Reposted by Karel "CaCO3" Berka
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
0244
Reposted by Karel "CaCO3" Berka
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...
27328
Karel "CaCO3" Berka @krapnik.bsky.social · 26/06/2026
upgraded ;)
000
Karel "CaCO3" Berka @krapnik.bsky.social · 25/06/2026
#CompChem #CompChemSky #EduSky
200
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
360
Karel "CaCO3" Berka @krapnik.bsky.social · 15/06/2026
nice #alphafoldology gym for alternative structure prediction
040
Reposted by Karel "CaCO3" Berka
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
122
Reposted by Karel "CaCO3" Berka
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
616336
Karel "CaCO3" Berka @krapnik.bsky.social · 05/06/2026
jedna by byla fajn u detskeho hriste v Kozeluzske…
010
Karel "CaCO3" Berka @krapnik.bsky.social · 04/06/2026
another #alphafoldology tool - DeltaDiff - for prediction of mutant protein structures.
000
Karel "CaCO3" Berka @krapnik.bsky.social · 04/06/2026
pipeline for #alphafoldology pipeline for identification of PPIs
000
Reposted by Karel "CaCO3" Berka
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
082
Karel "CaCO3" Berka @krapnik.bsky.social · 28/05/2026
would it work on ORCA output as well?
100
Karel "CaCO3" Berka @krapnik.bsky.social · 27/05/2026
MD simulations are my favorite - otherwise I leave it up to Grammarly…
020
Karel "CaCO3" Berka @krapnik.bsky.social · 20/05/2026
any chance to beat human serum albumin assay one? ;)
000
Karel "CaCO3" Berka @krapnik.bsky.social · 19/05/2026
ja nemluvim o matematice, ale snalyticke chemii
110
Karel "CaCO3" Berka @krapnik.bsky.social · 19/05/2026
11,6 se zaokrouhluje nahoru. Dokonce v analytice nas kdysi davno ucili, ze se zaokrouhluje na suda cisla, takze pak by vychazelo na dvanactku i 11,5… ;)
120
Karel "CaCO3" Berka @krapnik.bsky.social · 19/05/2026
takze 66B?
010
Karel "CaCO3" Berka @krapnik.bsky.social · 18/05/2026
karlovarsky tam taky nikde nevidim
000
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
010
Karel "CaCO3" Berka @krapnik.bsky.social · 10/05/2026
wow, interesting data, but that “chemical and material scientists”divorce less than “clergy” is a bit unexpected… ;) #chemsky
031
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Sebastian Hiller on integrative NMR #pps2026
042
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Andrea Soranno on IDP biophysics #ppps2026
041
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Ahrum Son on protein structural changes in alzheimer’s disease #pps2026
021
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 07/05/2026
And great opening of Prague Protein Spring by David Baker @nd-bakerlab.bsky.social #pps2026
232
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 07/05/2026
Next speaker is Michele Vendruscolo on dugging undruggable #pps2026
041
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
Eugene Shakhnovich on chaperonines helping bacteia to resist antibiotics #pps2026
141
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
Patricia Clark on silent mutations and protein folding #pps2026
031
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
On neurodegeneration by Nikolay Dokholyan #pps2026
021
Reposted by Karel "CaCO3" Berka
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
042
Reposted by Karel "CaCO3" Berka
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
031
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 08/05/2026
Gennady Verkhivker on AI and allostery in protein kinases #pps2026
051
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Basile Wicky @ethz.ch on protein design #pps2026
041
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Tomas Pluskal @pluskal-lab.org on plants, their products and AI #pps2026
0113
Reposted by Karel "CaCO3" Berka
Vojtech Spiwok @spiwokv.bsky.social · 09/05/2026
Agnes Toth-Petroczy @tothpetroczylab.bsky.social on IDPs #pps2026
032
Reposted by Karel "CaCO3" Berka
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.
021
Reposted by Karel "CaCO3" Berka
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...
1293
Karel "CaCO3" Berka @krapnik.bsky.social · 05/05/2026
yeah, sending student’s certificates feedback automatically after filling course did that to me as well…
000