Karel "CaCO3" Berka
@krapnik.bsky.social
theoretical physical chemist, molecular modeller and chem- and bioinformatician - #AlphaFoldology enthusiast
Palacky University Olomouc, ORCID:0000-0001-9472-2589 #boardgamegeek (tweets my own) #ELIXIRCZ
Palacky University Olomouc, ORCID:0000-0001-9472-2589 #boardgamegeek (tweets my own) #ELIXIRCZ
V-rescale should be almost as easy as Berendsen and it works fine
October 6, 2025 at 6:29 PM
V-rescale should be almost as easy as Berendsen and it works fine
so it would make nice tool for teaching of molecular modelling bsky.app/profile/krap...
What would you use to setup and run a small MD simulations?
no HPC, just for teaching and few small systems for thinking on structures? maybe to test some small reactions…
#CompChemSky
no HPC, just for teaching and few small systems for thinking on structures? maybe to test some small reactions…
#CompChemSky
October 6, 2025 at 6:21 PM
so it would make nice tool for teaching of molecular modelling bsky.app/profile/krap...
this fake Nobel one is good as well
October 6, 2025 at 5:35 PM
this fake Nobel one is good as well
Today’s addition is also good
#JournalofImmaterialResearch
#JournalofImmaterialResearch
October 6, 2025 at 5:04 PM
Today’s addition is also good
#JournalofImmaterialResearch
#JournalofImmaterialResearch
Sounds fun - I’ll try it ;)
October 4, 2025 at 5:04 AM
Sounds fun - I’ll try it ;)
no proteins - small molecules.
in the olden days, I would use Hyperchem
in the olden days, I would use Hyperchem
October 1, 2025 at 3:15 PM
no proteins - small molecules.
in the olden days, I would use Hyperchem
in the olden days, I would use Hyperchem
October 1, 2025 at 3:09 PM
link na pořad zde: www.ceskatelevize.cz/porady/10969...
Viry vytvořené AI loví odolné bakterie - 25. září 09:00 - Studio 6 | Česká televize
Karel Berka
www.ceskatelevize.cz
September 25, 2025 at 1:23 PM
link na pořad zde: www.ceskatelevize.cz/porady/10969...
CryoEM - 2017 Dubochet, Frank, Henderson www.nobelprize.org/prizes/chemi...
Press release: The 2017 Nobel Prize in Chemistry - NobelPrize.org
www.nobelprize.org
September 22, 2025 at 7:35 PM
CryoEM - 2017 Dubochet, Frank, Henderson www.nobelprize.org/prizes/chemi...
Alphafold is great, but newer #Alphafoldology tools such as RFdiffusion, Boltz-2, Chai, or BindCraft would be even nicer…
September 18, 2025 at 2:46 PM
Alphafold is great, but newer #Alphafoldology tools such as RFdiffusion, Boltz-2, Chai, or BindCraft would be even nicer…
more structural bioinfo modules would be great though - e.g. boltz-2 would be great.
September 16, 2025 at 6:08 PM
more structural bioinfo modules would be great though - e.g. boltz-2 would be great.
second possibility might be nextflow - I know that @pdbeurope.bsky.social is going to organize all annotations from PDBe-KB as nextflow modules so that the loop to update annotations should shorten to - annotated as are published (ASAP)
September 16, 2025 at 6:07 PM
second possibility might be nextflow - I know that @pdbeurope.bsky.social is going to organize all annotations from PDBe-KB as nextflow modules so that the loop to update annotations should shorten to - annotated as are published (ASAP)
well - you can prepare modules FOR usegalaxy.eu (similarly to alphafold2 module) and then it should be doable.
Galaxy
Galaxy is a community-driven web-based analysis platform for life science research.
usegalaxy.eu
September 16, 2025 at 6:00 PM
well - you can prepare modules FOR usegalaxy.eu (similarly to alphafold2 module) and then it should be doable.
takže číslo z Malaysie?
September 16, 2025 at 5:18 PM
takže číslo z Malaysie?
will be full of golden nanoparticles in a form of bonbons for Night of Science next Friday ;)
September 16, 2025 at 5:13 PM
will be full of golden nanoparticles in a form of bonbons for Night of Science next Friday ;)
I had to add a little bit more intermolecular interaction though (with glue pistol) otherwise the model falls apart easily - best I could hold was trimer of dimers, definitively not all 24 subunits
September 16, 2025 at 4:52 PM
I had to add a little bit more intermolecular interaction though (with glue pistol) otherwise the model falls apart easily - best I could hold was trimer of dimers, definitively not all 24 subunits