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Karel "CaCO3" Berka

@krapnik.bsky.social

1.9K followers 4.7K following 530 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 · 2d

V-rescale should be almost as easy as Berendsen and it works fine

Karel "CaCO3" Berka @krapnik.bsky.social · 2d

so it would make nice tool for teaching of molecular modelling bsky.app/profile/krap...

Karel "CaCO3" Berka @krapnik.bsky.social · 7d

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

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Karel "CaCO3" Berka @krapnik.bsky.social · 2d

Yes, please!

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Karel "CaCO3" Berka @krapnik.bsky.social · 2d

this fake Nobel one is good as well

Karel "CaCO3" Berka @krapnik.bsky.social · 2d

Today’s addition is also good
#JournalofImmaterialResearch

Journal of Immaterial research
awarded RFK Jr.
“for taking bold action to reduce life expectancy in the USA”

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Karel "CaCO3" Berka @krapnik.bsky.social · 4d

any easy GUI?

Karel "CaCO3" Berka @krapnik.bsky.social · 4d

Sounds fun - I’ll try it ;)

Karel "CaCO3" Berka @krapnik.bsky.social · 5d

Tessera iacta est. #volby2025

Karel "CaCO3" Berka @krapnik.bsky.social · 7d

no proteins - small molecules.

in the olden days, I would use Hyperchem

Karel "CaCO3" Berka @krapnik.bsky.social · 7d

@livecomsjournal.bsky.social ?

Karel "CaCO3" Berka @krapnik.bsky.social · 7d

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

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Karel "CaCO3" Berka @krapnik.bsky.social · 13d

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

Karel "CaCO3" Berka @krapnik.bsky.social · 13d

K dnešnímu vystoupení ve Studiu 6 na @ceskatelevize.cz jsem si přichystal #3Dprint pomůcku - model bakteriofága phiX174, jenž posloužil @arcinstitute.org k přípravě nových bakteriofágů proti rezistentním kmenům E. coli

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Karel "CaCO3" Berka @krapnik.bsky.social · 16d

CryoEM - 2017 Dubochet, Frank, Henderson www.nobelprize.org/prizes/chemi...

Press release: The 2017 Nobel Prize in Chemistry - NobelPrize.org

www.nobelprize.org

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Karel "CaCO3" Berka @krapnik.bsky.social · 20d

Alphafold is great, but newer #Alphafoldology tools such as RFdiffusion, Boltz-2, Chai, or BindCraft would be even nicer…

Karel "CaCO3" Berka @krapnik.bsky.social · 22d

more structural bioinfo modules would be great though - e.g. boltz-2 would be great.

Karel "CaCO3" Berka @krapnik.bsky.social · 22d

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)

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Karel "CaCO3" Berka @krapnik.bsky.social · 22d

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

Karel "CaCO3" Berka @krapnik.bsky.social · 22d

takže číslo z Malaysie?

Karel "CaCO3" Berka @krapnik.bsky.social · 22d

will be full of golden nanoparticles in a form of bonbons for Night of Science next Friday ;)

Karel "CaCO3" Berka @krapnik.bsky.social · 22d

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

Karel "CaCO3" Berka @krapnik.bsky.social · 22d

today #3Dprint protein is ferritin (PDB: 6I36)

available here:
www.printables.com/model/141627...

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Karel "CaCO3" Berka @krapnik.bsky.social · 29d

uz?

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Reposted by Karel "CaCO3" Berka

Kate Michie @kmichie.bsky.social · Jul 24

🧬🧶

ChimeraX @chimerax.ucsf.edu · Jul 24

ChimeraX daily builds can predict binding affinity of small molecules using Boltz 2 on your Mac, Windows or Linux computer. www.rbvi.ucsf.edu/chimerax/dat...

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Karel "CaCO3" Berka @krapnik.bsky.social · Jul 18

I guess it was due to large enough quantity to isolate myoglobin (it was before restriction endonucleases that enabled protein production in cell cultures)