Karel "CaCO3" Berka

cool tuning of protein language models to individual families with ProteinTTT #Alphafoldology

fake Nobel prize for Donald Trump

He did it!

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...

Yes, please!

fake Nobel prize in Ecology 2025

this fake Nobel one is good as well

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

Today’s addition is also good
#JournalofImmaterialResearch

any easy GUI?

Sounds fun - I’ll try it ;)

Tessera iacta est. #volby2025

no proteins - small molecules.

in the olden days, I would use Hyperchem

@livecomsjournal.bsky.social ?

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

Viry vytvořené AI loví odolné bakterie - 25. září 09:00 - Studio 6 | Česká televize Karel Berka

link na pořad zde: www.ceskatelevize.cz/porady/10969...

bacteriophage phiX174 #3Dprint model

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

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…

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)

well - you can prepare modules FOR usegalaxy.eu (similarly to alphafold2 module) and then it should be doable.

takže číslo z Malaysie?

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

ferritin 3d model

ferritin 3d model open

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

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

uz?

🧬🧶

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

All our reports and sequences are available at virus.img.cas.cz

🧬 & 🖥️

Developing molecular surveillance of SARS-CoV-2 in the Czech Republic (2021-2022) - PubMed Molecular surveillance was widely used during the COVID-19 pandemic to detect rapidly emerging variants and monitor the transmission of SARS-CoV-2 within communities. In 2021, the Czech COVID-19 Genom...

+1

This paper is based on our experience on how Czech research teams offered their bioinformatics expertise to public health needs and coordinate within COG-CZ inofficial consortia. We started without funding and in biweekly reports monitored the COVID pandemics.

pubmed.ncbi.nlm.nih.gov/40467653/