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jankosinski.bsky.social @jankosinski.bsky.social · Aug 22

⏰ URGENT! ⏰ Into structural modeling, design, integration with experiments, evolution, or platforms? Join our conference, share your work, and see what’s hot! Only 4 days left to submit your abstract! 👇

EMBL Events @events.embl.org · Jul 24

Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻

Find out about molecular modelling to systems-level analyses and evolution, and more.

Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl

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EMBL Events @events.embl.org · Jul 24

Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻

Find out about molecular modelling to systems-level analyses and evolution, and more.

Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl

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jankosinski.bsky.social @jankosinski.bsky.social · Jul 28

One month remaining to register for our conference!

Have a look at the outstanding speakers and programme, and use the link to join the 2nd edition of the Computational Structural Biology Conference in Heidelberg!

EMBL Events @events.embl.org · Jul 24

Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻

Find out about molecular modelling to systems-level analyses and evolution, and more.

Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl

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jankosinski.bsky.social @jankosinski.bsky.social · May 30

Check out HMFF and Mosaic on GitHub: (7/n)
🔗 github.com/KosinskiLab/...

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jankosinski.bsky.social @jankosinski.bsky.social · May 30

HMFF comes with Mosaic, a software ecosystem for membrane segmentation, refinement, HMFF simulations, and morphometrics. (6/n) 🔗https://github.com/KosinskiLab/mosaic

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jankosinski.bsky.social @jankosinski.bsky.social · May 30

For example, it allows building models like this filamentous influenza A virion ⬇️ (5/n)

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jankosinski.bsky.social @jankosinski.bsky.social · May 30

HMFF aids in on-membrane particle picking, supports multiscale modeling, and allows backmapping to atomic detail (4/n)

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jankosinski.bsky.social @jankosinski.bsky.social · May 30

This enables physically realistic and complete membrane models of cells, organelles, and viruses, consistent with experimental data (3/n)

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jankosinski.bsky.social @jankosinski.bsky.social · May 30

Helfrich Monte Carlo Flexible Fitting (HMFF) optimizes membrane models directly in electron microscopy densities (2/n)

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jankosinski.bsky.social @jankosinski.bsky.social · May 30

New method toward modeling cells and viruses! HMFF enables integrative membrane modeling and simulation guided by electron microscopy data. Created by Valentin Maurer and Marc Siggel @embl.org ‪‪@cssbhamburg.bsky.social‬, in collaboration with @WPezeshkian lab (1/n) www.biorxiv.org/content/10.1...

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Eva Kowalinski @kowaeva.bsky.social · Apr 16

Are you a postdoc ready for transition to an independent position? You connect infection biology with cutting-edge structural biology or multimodal imaging? Are you aware of such a colleague?

I am seeking speakers for "The Next Generation in Infection Biology" microsymposium on June 6 2025.

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Centre for Structural Systems Biology CSSB @cssbhamburg.bsky.social · Apr 4

28 children spent the day at CSSB for Girls' and Boys' Day yesterday! The kids built microscopes, conducted chemistry and chromatography experiments, tried VR goggles and much more.

@carobarisch.bsky.social @landaulabcssb.bsky.social @jankosinski.bsky.social @topf-lab.bsky.social

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jankosinski.bsky.social @jankosinski.bsky.social · Mar 29

Great work led by our PhD student Iuliia Kotova in collaboration with Fan Liu @fan-liu.bsky.social, Boris Bogdanow, Lars Mühlberg, and Olivier Duss @olivierduss.bsky.social and Guelsah Gabriel labs. Structural analysis by our PhD student Konstantin Gilep.
www.biorxiv.org/content/10.1...

Snapshot of in-cell protein contact sites reveals new host factors and hijacking of paraspeckles during influenza A virus infection

Influenza A virus (IAV) exploits the host cellular machinery to facilitate its replication, yet many host-IAV interactions remain unexplored in the cellular context. Detailed information about interac...

www.biorxiv.org

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jankosinski.bsky.social @jankosinski.bsky.social · Mar 29

We captured a snapshot of in-cell protein contact sites during influenza A virus infection. In-cell crosslinking, AlphaFold modeling, and functional follow-ups revealed new host factors and mechanisms. A step toward modeling the infected cell.

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jankosinski.bsky.social @jankosinski.bsky.social · Mar 28

Sorry Albert, I can't have coffee with you today because time is relative, and mine just ran out. #chatgpt4o

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jankosinski.bsky.social @jankosinski.bsky.social · Mar 27

yeah, it went bananas

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jankosinski.bsky.social @jankosinski.bsky.social · Mar 27

Draw a ribbon representation of a protein structure shaped like a banana, with alpha-helices, beta-sheets, and loops clearly visible, maintaining realistic molecular geometry and coloring styles typical for protein visualizations.

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EMBL Events @events.embl.org · Feb 24

Join us in Heidelberg for the 2nd edition of #EMBOComp3D! 🧬

Explore cutting-edge AI-driven innovations and classical methods in biomolecular research, new sessions on drug design, and make contacts during the job fair. Submit your abstract by 26 Aug 👉 s.embl.org/csb25-01-bl

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EMBL Events @events.embl.org · Feb 6

⏰ You have until 3 March to submit your abstract and be part of #EESInfection ➡️ https://s.embl.org/ees25-04-bl

🦠 🍄 This symposium will bring together researchers working on different pathogens and pave the way for new strategies to overcome current challenges in the treatment of infections 💡

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jankosinski.bsky.social @jankosinski.bsky.social · Feb 9

"We demonstrate that current co-folding approaches largely memorise ligand poses from their training data, hindering their use for de novo drug design."

Peter Škrinjar @peterskrinjar.bsky.social · Feb 8

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!

www.biorxiv.org/content/10.1...

🧵👇 (1/n)

Have protein-ligand co-folding methods moved beyond memorisation?

Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...

www.biorxiv.org

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Jan 17

PDB-IHM (formerly PDB-Dev) is for integrative structures.

Intergrative structures = from multiple experimental & computational methods.
Since mid-2024 assigned PDB ids & DOIs.

Access via wwPDB archive or
PDB-IHM - pdb-ihm.org

👉 https://www.wwpdb.org/news/news?year=2025#677880ea44a8c95814022eb9

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Ezgi Karaca @ezgikaraca.bsky.social · Jan 2

The legendary EMBO Integrative Modeling Course is back! If you want to be in this picture in the 2025 edition, just go ahead and register at meetings.embo.org/event/25-bio...

Organized by myself & @amjjbonvin.bsky.social & @arneelof.bsky.social & @lindorfflarsen.bsky.social

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Peter Koo @pkoo562.bsky.social · Dec 10

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jankosinski.bsky.social @jankosinski.bsky.social · Dec 8

"Challenges along the way, but it worked out in the end" youtu.be/HnT1VWzdFWc?...

2024 Nobel Prize lectures in chemistry | David Baker, Demis Hassabis and John Jumper

YouTube video by Nobel Prize

youtu.be

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jankosinski.bsky.social @jankosinski.bsky.social · Dec 8

Perhaps this is not the only time this picture will be shown during a Nobel Prize lecture 😉

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