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
cool tuning of protein language models to individual families with ProteinTTT #Alphafoldology
ProteinTTT enables *customizing* protein language models to one target protein at a time without assuming any additional data via on-the-fly self-supervised fine-tuning on the single protein
October 24, 2025 at 2:53 AM
cool tuning of protein language models to individual families with ProteinTTT #Alphafoldology
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 1, 2025 at 3:04 PM
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
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
September 25, 2025 at 1:22 PM
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
September 16, 2025 at 4:48 PM
Reposted by Karel "CaCO3" Berka
🧬🧶
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...
July 24, 2025 at 3:06 AM
🧬🧶
+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/
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/
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...
pubmed.ncbi.nlm.nih.gov
June 19, 2025 at 5:02 PM
+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/
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/
On personal #Alphafoldology notice - I’ve got my Professorship in Biomolecular Chemistry and Structural Biology today.
June 16, 2025 at 2:13 PM
On personal #Alphafoldology notice - I’ve got my Professorship in Biomolecular Chemistry and Structural Biology today.
Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀
June 6, 2025 at 7:11 PM
#ELIXIRAHM 2025 in Thessaloniki started with bold vision
June 2, 2025 at 11:34 AM
#ELIXIRAHM 2025 in Thessaloniki started with bold vision
Can AF2-predicted protein structures be used to determine the protein–ligand complex with the same degree of confidence as experimentally determined protein structures?
🔗 ccdc-info.com/4dyNBxj
#DrugDiscovery #CompChemSky
🔗 ccdc-info.com/4dyNBxj
#DrugDiscovery #CompChemSky
May 29, 2025 at 10:56 AM
I got weird #3Dmissprint on @prusa3d.com MK3.9 when printing 3D periodic tables from PLA (no supports needed)
I got one printer head stuck with filament all over and on the second I was able to stop the print when this weird behavior occured:
I got one printer head stuck with filament all over and on the second I was able to stop the print when this weird behavior occured:
May 24, 2025 at 7:54 PM
I got weird #3Dmissprint on @prusa3d.com MK3.9 when printing 3D periodic tables from PLA (no supports needed)
I got one printer head stuck with filament all over and on the second I was able to stop the print when this weird behavior occured:
I got one printer head stuck with filament all over and on the second I was able to stop the print when this weird behavior occured:
Scoring #Alphafoldology with AF3score
AF3Score: A Score-Only Adaptation of AlphaFold3 for Biomolecular Structure Evaluation [new]
AlphaFold3 scores biomolecular complexes directly, bypassing refinement for structure eval.
AlphaFold3 scores biomolecular complexes directly, bypassing refinement for structure eval.
May 18, 2025 at 2:39 PM
Scoring #Alphafoldology with AF3score
skoda, ze cesky ty zakladni cislovky tak pekne nezni…
The new pope has a maths degree.
Finally—a Pontiff who really knows his cardinal numbers
Finally—a Pontiff who really knows his cardinal numbers
May 9, 2025 at 11:10 AM
skoda, ze cesky ty zakladni cislovky tak pekne nezni…
Nice short primer to basic #Alphafoldology tools
Cutting-edge tools for structural biology: bringing AlphaFold to the people: Trends in Microbiology https://www.cell.com/trends/microbiology/fulltext/S0966-842X(25)00110-6?rss=yes
Cutting-edge tools for structural biology: bringing AlphaFold to the people
The recent application of artificial intelligence-based prediction of protein and protein complex structures by AlphaFold has revolutionized biology. Here, we give an overview of the tools that make this revolution accessible to experimental microbiologists without training in bioinformatics or sophisticated computer equipment, and show how this helps to gain new insights.
www.cell.com
May 5, 2025 at 4:57 AM
Nice short primer to basic #Alphafoldology tools
Reposted by Karel "CaCO3" Berka
Moldina is freely available at github.com/It4innovatio...
GitHub - It4innovations/moldina-multiple-ligand-molecular-docking-over-autodock-vina
Contribute to It4innovations/moldina-multiple-ligand-molecular-docking-over-autodock-vina development by creating an account on GitHub.
github.com
May 2, 2025 at 9:07 AM
Moldina is freely available at github.com/It4innovatio...
Largest #Alphafoldology study so far…
Clustering 821M structures (AFDB&ESMatlas) into 5.12M groups reveals biome-specific groups but only 1 new fold (many novel domain combinations though!).
@jingiyeo.bsky.social @yewonhan.bsky.social @nbordin.bsky.social @hbkgenomics.bsky.social @milot.bsky.social @martinsteinegger.bsky.social
@jingiyeo.bsky.social @yewonhan.bsky.social @nbordin.bsky.social @hbkgenomics.bsky.social @milot.bsky.social @martinsteinegger.bsky.social
April 30, 2025 at 12:22 PM
Largest #Alphafoldology study so far…
@olinium42.bsky.social o popularizaci chemie právě teď na www.youtube.com/live/bjqJ1_y...
Olga Ryparová (Olinium) Od molekul k lidem: Chemie, která inspiruje
YouTube video by Katedra fyzikální chemie UPOL
www.youtube.com
April 30, 2025 at 12:09 PM
@olinium42.bsky.social o popularizaci chemie právě teď na www.youtube.com/live/bjqJ1_y...
V Kutné hoře dnes ráno nebyla ani noha…
April 21, 2025 at 1:48 PM
V Kutné hoře dnes ráno nebyla ani noha…
KULL #Alphafoldology to generate conformations to see side-chain dynamics with #AF2
AlphaFold is amazing but gives you static structures 🧊
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
April 18, 2025 at 12:13 PM
KULL #Alphafoldology to generate conformations to see side-chain dynamics with #AF2
so… which of preprint about AF3 at CASP16 should I read? @arneelof.bsky.social
this one on @biorxivpreprint.bsky.social
or the other on
@authorea.com ?
this one on @biorxivpreprint.bsky.social
or the other on
@authorea.com ?
AlphaFold3 at CASP16 | bioRxiv https://www.biorxiv.org/content/10.1101/2025.04.10.648174v1
April 17, 2025 at 7:50 AM
so… which of preprint about AF3 at CASP16 should I read? @arneelof.bsky.social
this one on @biorxivpreprint.bsky.social
or the other on
@authorea.com ?
this one on @biorxivpreprint.bsky.social
or the other on
@authorea.com ?
Massive #Alphafoldology with MassiveFold
We are happy to announce the release of MassiveFold 1.5.0.
It is now possible to add post-translational modifications and to run ligand screening with AlphaFold3!
It is now possible to add post-translational modifications and to run ligand screening with AlphaFold3!
April 11, 2025 at 10:16 AM
Massive #Alphafoldology with MassiveFold
A new preprint from our lab at @fchupol.bsky.social
Pathogenicity Patterns in Cytochrome P450 Family https://www.biorxiv.org/content/10.1101/2025.03.30.646180v1
April 4, 2025 at 10:55 AM
A new preprint from our lab at @fchupol.bsky.social
Povedená chemická opera… youtu.be/jVN1utwXw0U?...
Chemická opera
YouTube video by FCH VUT
youtu.be
March 29, 2025 at 6:48 PM
Povedená chemická opera… youtu.be/jVN1utwXw0U?...