iiinova — where your digital self keeps evolving

Jan Gebauer @gebauer.bsky.social · 30/09/2026

Just returned from a small collagen symposium in Freiberg/Sachsen hosted by the FILK Freiberg institute. It was mostly steered towards application, with me being one voice of the basic researchers. It was interesting to see a completly different crowd working on a different aspect of collagens!

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Jan Gebauer @gebauer.bsky.social · 08/07/2026

Ich teile selten so was, aber diese hier halte ich aber für extrem wichtig für den Erhalt unserer Demokratie - und ich befürchte nicht viele interessiert es ...😬 (🇬🇧 in Germany there is massive attack on transparency by the current goverment...) 👇 #IFG weact.campact.de/petitions/sp...

weact.campact.de

SPD, stoppt den Frontalangriff auf die Informationsfreiheit!

Wir alle haben das Recht auf staatliche Informationen. Seit 2006 müssen Behörden auf Antrag nach dem Informationsfreiheitsgesetz (IFG) Dokumente herausgeben – seien es Verträge, interne Weisungen oder...

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Jan Gebauer @gebauer.bsky.social · 02/07/2026

Sylvie Ricard-Blum started the last workshop for today at #MBE2026 — a fabulous talk on known and maybe-not-yet-known interactions of endostatin, and the wider scope of PPIs in the ECM. Now eagerly waiting for the publication of the teased tool created in collab with @valerioizzi.bsky.social 😉

Sylvie Ricard-Blum giving a talk at Matrix Biologe Europe 2026

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Jan Gebauer @gebauer.bsky.social · 30/06/2026

The UniProt database has network problems for the second time in 3 weeks. Anyone know anything? This DB is so essential to a protein biochemist's daily work, I can hardly imagine working without it 😬 #biochemistry #protein

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Jan Gebauer @gebauer.bsky.social · 30/06/2026

Workshop #1 at #MBE2026 featured @tranejoan.bsky.social and @collagenyoshi.bsky.social back-to-back: first a wonderful talk on collagen trafficking, then a deep dive into lysine hydroxylation in collagens — asking the important question of how lysyl hydroxylases recognise their specific targets.

Joan Chang giving a talk at MBE 2026 in Oulu.

Yoshihiro Ishikawa giving a talk at MBE 2026 in Oulu.

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Jan Gebauer @gebauer.bsky.social · 30/06/2026

@nabalabuic.bsky.social starts the second day at #MBE2026. I already spotted the first protein structure so I am in 😉

Alexandra Naba giving a talk a the MBE 2026 in Oulu.

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Jan Gebauer @gebauer.bsky.social · 29/06/2026

Looking forward to it 😉

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Reposted by Jan Gebauer

Joan Chang @tranejoan.bsky.social · 29/06/2026

What a wonderful first #ECR session hosted by @themeshwork.bsky.social! Join in the vibrant community and the future of #ECMatrix is super bright! #MBE2026

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Jan Gebauer @gebauer.bsky.social · 29/06/2026

Just arrived at #MBE2026 in time for Fiona Watt's talk. Missed @valerioizzi.bsky.social's intro and the first session though — today literally every part of my transport chain was delayed 🤷 Looking forward to an exciting week of science at beautiful @oulu.fi.

A photo of a conference notebook and a sticker of Oulu University, as given to every conference participant.

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Jan Gebauer @gebauer.bsky.social · 26/06/2026

Yesterday on my way to work... Who else thinks "Astrid Lindgren"? 🤣

A man rides an e-scooter away from the camera down a gravel park path on a sunny day, a large metal floor fan strapped to his back like a backpack, its blades spinning.

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Jan Gebauer @gebauer.bsky.social · 21/06/2026

This year's #crystallography course is in full swing. We swapped experimental phasing for #NMR and, for the first time, local #AlphaPulldown. But the real essential for an IT-heavy course is the snacks — and we're well stocked.

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Jan Gebauer @gebauer.bsky.social · 07/07/2025

First full day of the #GRC #Collagen, obviously can't share anything, but there were already amazing talks!

Photo into the lecture hall of for the GRC Collagen

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Jan Gebauer @gebauer.bsky.social · 09/06/2025

This sounds really interesting! Eager to test it with some structures we have lying around. 👍

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Jan Gebauer @gebauer.bsky.social · 12/05/2025

Okay, it's officially summer in Cologne, when I have to move our CryoEM machine from my office to an air conditioned room... ☀️(In Winter I am using it's heat for saving a little on heaters)

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Reposted by Jan Gebauer

Richard M. Carpiano, PhD, MPH @rmcarpiano.medsky.social · 16/04/2025

Do we really age in bursts like that recent study suggests? @drjenndowd.bsky.social yet again provides a terrific overview and explainer of that study. 🛟🧪 medsky 😷demography sociology

jenndowd.substack.com

Are we really aging in bursts?

If you are nearing 44 or 60, don't panic.

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Jan Gebauer @gebauer.bsky.social · 16/04/2025

Thanks for this! The study was all over the news in Germany, but somehow I never cared to check. As a scientist myself I really should have 🙄 Overselling scientific findings is really a problem in our days - it decreases trust in the scientific process...

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Jan Gebauer @gebauer.bsky.social · 12/04/2025

Und ich dachte es sei ein Witz... 😂 Olli glaube ich auch, oder zumindest hat er so getan...

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Jan Gebauer @gebauer.bsky.social · 08/04/2025

There is an #science feed and #ML in structural biology feed, but is there an protein #crystallography feed? And if not would we need one 🤔

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Jan Gebauer @gebauer.bsky.social · 08/04/2025

Only have some slides to explain protein domains and the importance to predict those to a public audience. Not sure if those help... 🤷‍♂️

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Jan Gebauer @gebauer.bsky.social · 08/04/2025

Full ack... Sadly the AI proponents often do not share our caution 😉

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Jan Gebauer @gebauer.bsky.social · 07/04/2025

I see your point, but I've heard this argument to often. "AF is different? - maybe just an important different confomer!" I do agree that crystal artefact exists and maybe this one deviation is upsold a little bit in the article, but in principle it's important to strengthen experimental strubio.

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Jan Gebauer @gebauer.bsky.social · 06/04/2025

Is Folding@Home still a thing? I have the impression neuronal network based methods have outpaced the energy based prediction software so far....or did they change the basis for the client? 🤔

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Jan Gebauer @gebauer.bsky.social · 04/04/2025

Not so fond of the war theme, but I agree with the message👍. I see so many projects just doing fancy -omics, trying to solve mechanisms - but sometimes you just have to get your hands dirty and purify that f*** protein.

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Jan Gebauer @gebauer.bsky.social · 02/04/2025

room for improvement - it is an essential part of the scientific progress... So, is this just me?

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Jan Gebauer @gebauer.bsky.social · 02/04/2025

Don't get me wrong, the study seems legit and I am eager to dig into it. Although every bit of focus on collagens research is great. But I don't like this "new" trend on reporting on practically unpublished results. I think we have a peer-review system for a reason and while there might be (2/n)

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Jan Gebauer @gebauer.bsky.social · 02/04/2025

I am a structural biologist working with collagens, so naturally I am very interested. I only had time to skim over the paper, but I have to admit I currently fail to see why this is _major_ news. Especially, as it is not yet peer-reviewed. I frankly have more questions than answers (1/n)

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Jan Gebauer @gebauer.bsky.social · 29/03/2025

I have the feeling that we lived in the golden age of medicine, already before AF. Knockouts mice, crispr/cas, mRNA vacs.These are all tremendous developments - independent of AF. Don't get me wrong: I am a structural biologist and use AF every day. It's great, but medicine was great already before

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Reposted by Jan Gebauer

DGMB @matrixbiologie.bsky.social · 28/03/2025

Congratulations to this year’s winner of the Young Investigator Award: Kristina Bubb from Cologne! @nystromlab.bsky.social

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Jan Gebauer @gebauer.bsky.social · 10/03/2025

Thanks! Finally I found it... 🥰 Somehow, expected it would be coot-1 or something along that line...

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Jan Gebauer @gebauer.bsky.social · 09/03/2025

Hi, could you please add me to the science feed? I am a structural biologist. You'll find the University facility I supervise here px.uni-koeln.de and papers on my own page Gebauer.koeln thanks a lot!

px.uni-koeln.de

RG Baumann

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Jan Gebauer @gebauer.bsky.social · 09/03/2025

I also thought about protein structures, but there is no left-handed alpha helix 🤔 but maybe that's the point? On the other hand the zigzag is not disordered... Frankly no idea... From which science area is it?

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Jan Gebauer @gebauer.bsky.social · 09/03/2025

And still, it's relatively often wrong - at least for protein complexes 😉

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Reposted by Jan Gebauer

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 08/03/2025

I added support for Boltz1 so we can calculate ipSAE and other scores for pairwise protein-protein interactions on AF2, AF3, and Boltz1 models. Will add nucleic acids eventually. github.com/DunbrackLab/...

github.com

GitHub - DunbrackLab/IPSAE: Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3

Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3 - DunbrackLab/IPSAE

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Jan Gebauer @gebauer.bsky.social · 09/03/2025

This sounds interesting and maybe exactly what I need. Plan to di some screening with #AF3 and a proper implementation ofna scoring function was still missing 👍 thanks!

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Jan Gebauer @gebauer.bsky.social · 09/03/2025

It might be a stupid question, but given I have installed coot 1 via ccp4 on WSL how do I run it? Couldn't find an executable anywhere...

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Jan Gebauer @gebauer.bsky.social · 05/03/2025

BMC has a solid JIF and welcomes all scientifically valid studies—so write up your story now and submit! 📩 DM me if you have questions or check out www.biomedcentral.com/collections/... #ExtracellularMatrix #ECM #CellBiology #CallForPapers #StructuralBiology [2/2]

biomedcentral.com

Call for papers - The Extracellular Matrix

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Jan Gebauer @gebauer.bsky.social · 05/03/2025

Get your data out now! 🚀 BMC has a special edition on “The Extracellular Matrix,” and I’m honoured to guest edit. We’re accepting manuscripts on all aspects of ECM, but if you know my background, you’ll know I’m especially excited about structural data and collagens 😉. [1/2]

biomedcentral.com

Call for papers - The Extracellular Matrix

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Jan Gebauer @gebauer.bsky.social · 18/02/2025

Sorry, but this is a gross misrepresentation of Alphafold and FoldIt. Google did put together some old ideas (amino acid coevolution), some brilliant ideas about neural networks and a LOT of computer power to solve the problem. AFAIK they never used FoldI(the game), but CASPnto judge their result.

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Jan Gebauer @gebauer.bsky.social · 31/01/2025

Wow, wasn't even aware, that the genbank was ever distributed by CD-ROM 😲

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Jan Gebauer @gebauer.bsky.social · 29/12/2024

A worrying talk about the (planned) deregulation of synthetic biology by the EU commision (and worldwide) from Margret Engelhard (from BfN ) at the #38C3. I am working with GMOs daily, but IN the lab and I am not a fan of releasing them ... media.ccc.de/v/38c3-let-s...

media.ccc.de

Let's build dodos! How generative AI is upturning the world of synthetic biology and hopelessly overwhelming traditional governance instruments.

Have you always wanted to build an egg-laying woolly milk sow or bring the legendary dodo back to life? The dream of some biologists to ...

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Jan Gebauer @gebauer.bsky.social · 11/12/2024

And we won! 🕺🎉 We got a neck massage device. 😂

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Jan Gebauer @gebauer.bsky.social · 11/12/2024

We have an annual window decoration competition in our biochemical institute. This is our contribution - I think it represents our group very nicely. #StructuralBiology #XMAS #XRAY #CryoEM

A window decoration stating merry xmas or - as an alternative reading - merry xmas written with 3D printed PDB letters. There is more StruBio related decoration.

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Jan Gebauer @gebauer.bsky.social · 05/12/2024

We have our own project which do incorporate all those aspects, but their are way to difficult for an annual 4 wks master course... 🙄

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Jan Gebauer @gebauer.bsky.social · 05/12/2024

Is anyone aware of a good model system, maybe a protein-interaction, which can be investigated by these methods? I guess it should be small enough for NMR, easy to crystalise (and produce) and maybe some interesting modelling/docking question.

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Jan Gebauer @gebauer.bsky.social · 05/12/2024

We are thinking of reorganising our #MX Master course to integrate a bigger variety of #structuralbiology. Namely #crystallography, #modelling and #NMR (our CryoEM guys still want to do their own thing 😉).

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Jan Gebauer @gebauer.bsky.social · 30/11/2024

Indeed it does! Unfortunately there is only part of the complex we aimed for...

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