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Charles University Structural Bioinformatics Group

@cusbg.bsky.social
394 followers 344 following 30 posts

Research group at the intersection of structural bioinformatics 🧬 and machine learning 🤖. Developing prankweb.cz, apoholo.cz, rnacentral.org/r2dt Lab: bioinformatics.cuni.cz/cusbg Heads: @davhox.bsky.social & @majek.bsky.social

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Reposted by Charles University Structural Bioinformatics Group
IOCB Tech @iocbtech.bsky.social · 21/05/2026
Czech biotech stands on stronger foundations than many still assume. Nearly 430 entities, CZK 97.5bn in annual revenue, and growing investor attention show real momentum. But further growth will depend on one thing: turning strong science into investable, scalable projects. #Biotech #Czechia
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Karel "CaCO3" Berka @krapnik.bsky.social · 28/04/2026
Artistic beauty of protein structures by @irinabezsonova.bsky.social
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Elixir of Progress @elucidating.extradimensional.space · 13/04/2026
This article is wild. The asteroid Bennu contains enough amino acid variety to construct a metabolism. A highly limited amino acid library from asteroid Bennu yields wide-ranging protein folds | Nature Communications
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A highly limited amino acid library from asteroid Bennu yields wide-ranging protein folds - Nature Communications
The origins of life are steeped in mystery, but the AI revolution could transform this field. Here, the authors use AI-based protein design software to uncover a broad range of protein folds that can be formed from small, primordial amino acid libraries constrained by asteroid and prebiotic chemistry data.
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Peter Škrinjar @peterskrinjar.bsky.social · 11/05/2026
Now published in NSMB! Paper: doi.org/10.1038/s415... Full PDF: rdcu.be/fhBtI Overview of additions since the preprint👇 (1/5)
doi.org
Evaluating generalization in protein–ligand cofolding methods - Nature Structural & Molecular Biology
This work introduces the Runs N’ Poses dataset for benchmarking deep learning methods on the protein–ligand complex prediction task. It shows that current methods rely on memorization, challenging the...
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Charles University, Faculty of Science @sciencecharles.bsky.social · 16/09/2025
🌿 The Botanical Garden of Charles University’s Faculty of Science turns 250! Founded in 1775, it is one of Central Europe’s oldest university gardens. Join us for a special anniversary program 15–21 Sept 2025. 🎉 @unikarlova.cuni.cz @botanickazahradauk.bsky.social
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Karel "CaCO3" Berka @krapnik.bsky.social · 16/09/2025
today #3Dprint protein is ferritin (PDB: 6I36) available here: www.printables.com/model/141627...
ferritin 3d modelferritin 3d model open
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CATH-Gene3D @cathgene3d.bsky.social · 16/09/2025
Kickstarting our symposium “Protein Annotations in the age of AI” at UCL!
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Adam Pecina @adampecina.bsky.social · 09/09/2025
We opened Day 2 of our #CECAM flagship workshop in Prague with the CECAM director Andrea Cavalli, highlighting steered #MD, dynamical docking & the complexity of binding energetics, and the challenges ahead. 🚀 #CECAMinPrague @iocbprague.bsky.social @cecamevents.bsky.social @iocbtech.bsky.social
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Gonzalo Parra @gonzaparra.bsky.social · 23/08/2025
CATH turns 30 years old 🥳 They celebrate with a Symposium on September 16th! I'll be presenting our work: "An Atlas of Energetic Evolutionary Constraints Across Protein Families" Unbelievable selection of speakers! So if you are around London, you can register to attend: tinyurl.com/2pnk8hj5
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Tomáš Pluskal @pluskal-lab.org · 21/08/2025
The first day of our bioML symposium at @iocbprague.bsky.social went very well. It is amazing to see how fast this field is moving forward. Thanks to everyone for the fantastic talks! 🤖🧬
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Radoslav Krivak @rdkbio.bsky.social · 27/06/2025
🚀 GPU-accelerated docking to P2Rank-predicted pockets
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Marian Novotny @majek.bsky.social · 19/06/2025
Fantastic to work with so many talented people! today at departmental conference of cell biology department of @sciencecharles.bsky.social . Many thanks to our guests from Israel for joining us and sharing their results and time with us
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Charles University Structural Bioinformatics Group @cusbg.bsky.social · 16/06/2025
Congratulations! 🎉
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Radoslav Krivak @rdkbio.bsky.social · 10/06/2025
🚀 Our paper on the updated PrankWeb, a web app for protein binding site prediction using P2Rank, is out in @narjournal.bsky.social. Now with docking integration! 👨‍💻 Try it: prankweb.cz 📄 Paper: doi.org/10.1093/nar/... 💻 GitHub: github.com/cusbg/prankweb Developed at @cusbg.bsky.social
Screenshot of PrankWeb.
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Dr Javier Sánchez Utgés @javierutges.bsky.social · 19/05/2025
I am #exhilarated to share that our new paper "LIGYSIS-web: a resource for the analysis of protein-ligand binding sites" is now published in @narjournal.bsky.social! After almost two years of development and more than 600 commits, LIGYSIS-web is out! 📜 : tinyurl.com/utges-LIGYSI...
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David Hoksza @davhox.bsky.social · 28/04/2025
Join us for the next #Bioinformatics seminar hosted by @sciencecharles.bsky.social and @mff.unikarlova.cuni.cz. Nora Martin from CRG : “How does the structure of a genotype-phenotype map shape variation and evolutionary processes?”. 📅 Wed, Apr 30 🕕 17:20 bioinformatics.cuni.cz/seminar
bioinformatics.cuni.cz
Binformatics seminar
Petr Daněček David Hoksza Marian Novotný
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Tomáš Pluskal @pluskal-lab.org · 11/04/2025
Back in July 2023 we organized a small bioML symposium at @iocbprague.bsky.social, and it turned out to be a very pleasant and successful event. This summer we are following up with a great line-up of speakers. Please register for free, deadline May 30. tinyurl.com/bioMLPrague25
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Gonzalo Parra @gonzaparra.bsky.social · 10/04/2025
3DSIG has now joined BlueSky!! Follow us there to keep building a strong community around the fields of Structural Bioinformatics and Computational Biophysics!
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Karel "CaCO3" Berka @krapnik.bsky.social · 04/04/2025
A new preprint from our lab at @fchupol.bsky.social
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Radoslav Krivak @rdkbio.bsky.social · 03/04/2025
🧪🇨🇿 A reminder: there’s a starter pack with Czech science institutions and research labs. A bunch of new ones have joined Bluesky lately -- and some, like Charles University (@charlesuni.cuni.cz), have fully made the move here from the other place.
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structbiocssb.bsky.social @structbiocssb.bsky.social · 22/03/2025
go.bsky.app/NaGFZwf
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Michal Kolář @mhko.bsky.social · 28/03/2025
Joe et al. have a fresh preprint on the MARTINI simulations of the #ribosome. arxiv.org/abs/2503.21357
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Karel "CaCO3" Berka @krapnik.bsky.social · 28/03/2025
we continue 1st @elixircz.bsky.social PhD conference with keynote by Martin Čech from @iocbprague.bsky.social and Cesnet on usegalaxy.cz
Galaxy intro by Martin Čech
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Karel "CaCO3" Berka @krapnik.bsky.social · 27/03/2025
1st @elixircz.bsky.social PhD conference at Telč on 27-28th March 2025 superthread.
conference is well attended ;)
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ELIXIR CZ @elixircz.bsky.social · 25/03/2025
🎉 #ELIXIRCZ celebrated 10 transformative years in life sciences! Thanks, everyone, for celebrating with us! 🥂 Cheers to a decade of growth & many more to come! #Science #Innovation #DataScience @elixir-europe.org www.elixir-czech.cz/news/10-year...
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Karel "CaCO3" Berka @krapnik.bsky.social · 27/03/2025
we continue 1st @elixircz.bsky.social PhD conference (I should made a hashtag - too late) with student presentations
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Marian Novotny @majek.bsky.social · 27/03/2025
We are grateful and fortunate to have Sameer Velankar, the head of @pdbeurope.bsky.social, to start first ever @elixircz.bsky.social phd conference. Thank you RSJ and @elixircz.bsky.social for general support!
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Karel "CaCO3" Berka @krapnik.bsky.social · 27/03/2025
we continue with keynote lecture by Sameer Velankar from @pdbeurope.bsky.social
Sameer Velankar speaks about PDBe
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Karel "CaCO3" Berka @krapnik.bsky.social · 27/03/2025
1st @elixircz.bsky.social PhD conference just started with @majek.bsky.social invitation
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European Conference on Computational Biology @eccb-europe.bsky.social · 25/03/2025
🎉 ECCB is now on Bluesky! Follow us for: ✔️ Latest conference updates ✔️ Key dates and calls ✔️ Networking & collaboration opportunities Join the ECCB community! #Bioinformatics #DataScience #CompBio
A poster to save the date for the upcoming ECCB 2026 on 31 August until 4 September 2026
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Adam Pecina @adampecina.bsky.social · 24/03/2025
🚀 Exciting news! We're organizing a @cecamevents.bsky.social Flagship Workshop on Quantum Chemistry in Drug Design in Prague, Sept 8–10, 2025! Join top experts from academia & industry. Few spots left for contributed talks! 📢 Apply now: www.cecam.org/workshop-det... #compchem #cadd #QM #CECAM
cecam.org
CECAM - Quantum Chemistry for Drug Design: From Theory to Applications
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Gonzalo Parra @gonzaparra.bsky.social · 22/03/2025
Everything comes to an end but memories remain!! We had a great 3DSIG/3DBioinfo event in "sunny" Barcelona this week!! I have enjoyed so much to help organising it & to have such great minds all together sharing science for 3 days!! Aufwiedersehen friends! For more science & friendships to come! ⭐
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Rafael Najmanovich @rnajmanovich.bsky.social · 22/02/2025
Happy to share our latest preprint. With NRGRank you can screen 1M in a day in a laptop (use our NEGSuite-Qt for that) - a billion compounds per day with our computational resources.
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Karel "CaCO3" Berka @krapnik.bsky.social · 04/03/2025
and key people behind establishment of the ELIXIR CZ setup
key supporters of ELIXIR CZ setup
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Marian Novotny @majek.bsky.social · 04/03/2025
@elixircz.bsky.social is celebrating 10th anniversary today! Jiri Vondrasek is in his summary acknowledging Janet Thornton and her contribution to founding of Elixir. Thank you!
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Gonzalo Parra @gonzaparra.bsky.social · 27/02/2025
Registration is open until March 6th!!
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Torsten Schwede @torstenschwede.bsky.social · 26/02/2025
🧪🧬🔬 Postdoc in Computational Structural Biology at the @biozentrum.unibas.ch & @sib.swiss in Basel, Switzerland. www.biozentrum.unibas.ch/open-positio... The position is initially funded for 3 years, possibility to start immediately. #StructurePrediction, #Bioinformatics, #Uniprot3D, #AI
Open Postdoc Position at the schwede lab, Biozentrum Basel.
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Carolina Sanchez-Rocha @caro-rocha.bsky.social · 25/02/2025
🚨 Unravel BILLIONS of years of protein evolution! 🚨 How did protein structures emerge and evolve over deep time? Join @zachary-ardern in the next ProSE Seminar! 📅 March 11, 3PM GMT 🔗 tinyurl.com/prose-seminar2 #ProteinEvolution #StructuralBiology
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Karel "CaCO3" Berka @krapnik.bsky.social · 26/02/2025
ROCKET #Alphafoldology fitting to lowres CryoEM to get conformation along the way
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Marian Novotny @majek.bsky.social · 06/02/2025
Counterintuitive
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Janani Durairaj (Jay) @ninjani.bsky.social · 20/02/2025
Join us tomorrow to hear @peterskrinjar.bsky.social talk about 🌹 Runs N' Poses 🌹! Curious to hear your thoughts on how to keep up with benchmarking in this field.
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Gonzalo Parra @gonzaparra.bsky.social · 13/02/2025
RT please: Just 1.5 months away from our joint 3DBioinfo/3DSIG amazing conference! These are our two great keynote speakers! @rolanddunbrack.bsky.social & @silviaosuna.bsky.social! Check our preliminary programme here: www.iscb.org/3dbioinfo202... Registration link: www.iscb.org/3dbioinfo202...
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David Hoksza @davhox.bsky.social · 16/02/2025
If you’re submitting to the @narjournal.bsky.social Web Server/Database issue and need to add PMC and DOI links to your #BibTeX as required—but the provided Perl script isn't working—I’ve created a small Python script to help you out! 🔗 github.com/davidhoksza/...
github.com
GitHub - davidhoksza/bibtex-pubmed-links: Adds PubMed/PMC/DOI links to BibTeX records
Adds PubMed/PMC/DOI links to BibTeX records. Contribute to davidhoksza/bibtex-pubmed-links development by creating an account on GitHub.
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Karel "CaCO3" Berka @krapnik.bsky.social · 16/02/2025
Important #AlphaFoldology thread about scoring intramolecular complexes in #AF2 and #AF3
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Anton Petrov @antonipetrov.bsky.social · 10/02/2025
🚀 New Paper Alert! 🚀 𝐑𝟐𝐃𝐓: a comprehensive platform for visualising RNA secondary structure Check it out in @narjournal.bsky.social: academic.oup.com/nar/article/... Here’s why you should give it a try 🧵👇
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Karel "CaCO3" Berka @krapnik.bsky.social · 13/02/2025
Excited to announce the upcoming @elixircz.bsky.social PhD Conference in #Bioinformatics, #Chemoinformatics, and #ComputationalBiology! Join us for 2 days of student presentations, a posters, and insightful discussions with distinguished scientists. 🧬https://bioinformatics.cuni.cz/phdconf2025
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Radoslav Krivak @rdkbio.bsky.social · 10/02/2025
How long does it take to predict ligand binding sites for all 220k proteins in the PDB? P2Rank 2.5 does it in 3 hours on a single CPU (16-core amd 5950x)—2x faster than the previous version 🚀. (1/n)
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Dr Javier Sánchez Utgés @javierutges.bsky.social · 07/02/2025
I didn't know that... Or did I? You can pretty much do anything in sequence and structure analysis with Jalview! ANYONE: "Hmmm, I wonder if I could cluster a group of sequences by features such as predicted ligand sites and then analyse amino acid conservation within each group..." 🤔 #JALVIEW: YES
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Janani Durairaj (Jay) @ninjani.bsky.social · 08/02/2025
We’ve been benchmarking deep learning co-folding methods for protein-ligand complex prediction, leading to the creation of 🌹Runs N’ Poses🌹. Great effort by @peterskrinjar.bsky.social and @jeeberhardt.bsky.social putting this together so quickly. Please have a look, excited for community feedback!
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