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
Reposted by Karel "CaCO3" Berka
We're hiring a 𝐓𝐫𝐚𝐢𝐧𝐢𝐧𝐠 𝐒𝐩𝐞𝐜𝐢𝐚𝐥𝐢𝐬𝐭 for 𝐀𝐥𝐩𝐡𝐚𝐅𝐨𝐥𝐝 𝐃𝐚𝐭𝐚𝐛𝐚𝐬𝐞 (AFDB)! Join our team to develop training content, create workshops, and drive global engagement with AlphaFold and AFDB.
Full-time, hybrid role.
Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
#AFDB #Jobs #emblebi
Full-time, hybrid role.
Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
#AFDB #Jobs #emblebi
January 26, 2026 at 10:55 AM
We're hiring a 𝐓𝐫𝐚𝐢𝐧𝐢𝐧𝐠 𝐒𝐩𝐞𝐜𝐢𝐚𝐥𝐢𝐬𝐭 for 𝐀𝐥𝐩𝐡𝐚𝐅𝐨𝐥𝐝 𝐃𝐚𝐭𝐚𝐛𝐚𝐬𝐞 (AFDB)! Join our team to develop training content, create workshops, and drive global engagement with AlphaFold and AFDB.
Full-time, hybrid role.
Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
#AFDB #Jobs #emblebi
Full-time, hybrid role.
Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
#AFDB #Jobs #emblebi
Our 9th Advanced in silico Drug Design workshop just started
- you can watch #9ADD at www.youtube.com/playlist?lis...
All materials will be available 9ADD workshop webpage> www.kfc.upol.cz/9add together with program
#compchemsky #chemsky #medchemsky 💊🧬🖥️
- you can watch #9ADD at www.youtube.com/playlist?lis...
All materials will be available 9ADD workshop webpage> www.kfc.upol.cz/9add together with program
#compchemsky #chemsky #medchemsky 💊🧬🖥️
9ADD - 9th Advanced Drug Design workshop 2026 - YouTube
9ADD workshop https://www.kfc.upol.cz/9add January 26, 2026 – January 30, 2026 Palacky University OlomoucThe 9ADD workshop focuses on using in silico tools a...
www.youtube.com
January 26, 2026 at 12:24 PM
Our 9th Advanced in silico Drug Design workshop just started
- you can watch #9ADD at www.youtube.com/playlist?lis...
All materials will be available 9ADD workshop webpage> www.kfc.upol.cz/9add together with program
#compchemsky #chemsky #medchemsky 💊🧬🖥️
- you can watch #9ADD at www.youtube.com/playlist?lis...
All materials will be available 9ADD workshop webpage> www.kfc.upol.cz/9add together with program
#compchemsky #chemsky #medchemsky 💊🧬🖥️
Reposted by Karel "CaCO3" Berka
If you develop software for research, consider responding to this survey trying to help understand who develops research software and how they work so as to get more robust support: softwaresaved.limequery.com/611257?lang=en #chemSky
2026 International RSE Survey
softwaresaved.limequery.com
January 23, 2026 at 8:14 PM
If you develop software for research, consider responding to this survey trying to help understand who develops research software and how they work so as to get more robust support: softwaresaved.limequery.com/611257?lang=en #chemSky
Reposted by Karel "CaCO3" Berka
An observation test for your inner 8-year-old.
You’ll be doing well to spot 12 deliberate mistakes.
From Treasure magazine, 1963
Official answers coming soon
(Even if you don’t reply, could you please ‘like’ or share this one?)
You’ll be doing well to spot 12 deliberate mistakes.
From Treasure magazine, 1963
Official answers coming soon
(Even if you don’t reply, could you please ‘like’ or share this one?)
January 24, 2026 at 8:17 AM
An observation test for your inner 8-year-old.
You’ll be doing well to spot 12 deliberate mistakes.
From Treasure magazine, 1963
Official answers coming soon
(Even if you don’t reply, could you please ‘like’ or share this one?)
You’ll be doing well to spot 12 deliberate mistakes.
From Treasure magazine, 1963
Official answers coming soon
(Even if you don’t reply, could you please ‘like’ or share this one?)
Reposted by Karel "CaCO3" Berka
Since Jan 1 2025, which feels like four trillion years ago, research has been shared on here 5 million whole-ass times. Bluesky recently passed 2 billion posts IN TOTAL.
So 0.25% of the entire site's traffic was citations to research.
That is actually massively high. Is it? Yes. Here's why.
So 0.25% of the entire site's traffic was citations to research.
That is actually massively high. Is it? Yes. Here's why.
January 8, 2026 at 1:08 PM
Since Jan 1 2025, which feels like four trillion years ago, research has been shared on here 5 million whole-ass times. Bluesky recently passed 2 billion posts IN TOTAL.
So 0.25% of the entire site's traffic was citations to research.
That is actually massively high. Is it? Yes. Here's why.
So 0.25% of the entire site's traffic was citations to research.
That is actually massively high. Is it? Yes. Here's why.
I am thinking about making several protein structure puzzle for computational proteomics course of @eubic-ms.org - which structures would you suggest and why?
January 6, 2026 at 7:25 PM
I am thinking about making several protein structure puzzle for computational proteomics course of @eubic-ms.org - which structures would you suggest and why?
Reposted by Karel "CaCO3" Berka
We are taking up a challenge with the #BEST-CSP blind test of predictions of physical properties of #molecular_crystals. Let's see what we can achieve before May. best-csp.eu #COSTactions #CompChem #PhysChem
Home - BEST-CSP | COST Action CA22107
BEST-CSP | COST Action CA22107. Bringing Experiment and Simulation Together in Crystal Structure Prediction.
https://best-csp.eu/#intro#COSTaction
December 23, 2025 at 9:42 AM
We are taking up a challenge with the #BEST-CSP blind test of predictions of physical properties of #molecular_crystals. Let's see what we can achieve before May. best-csp.eu #COSTactions #CompChem #PhysChem
Molecular PF 2026
December 26, 2025 at 10:02 PM
Molecular PF 2026
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...