Ezgi Karaca

We just bumped into something very preliminary… but very exciting:

AF2.3 and AF3.0 distograms may potentially reproduce MD-like behavior.

Until we do further tests, you can reach our early insights at www.biorxiv.org/content/10.1...

Meet the speakers of our anniversary symposium "Advances in Structural Analysis of Biomolecules: From Subcellular Imaging to Drug Design"

cbc-cpc2025.org

October 23-24, 2025, Berlin

Please like and share! #ChemBioPhys2025

Due to the high level of interest, we have decided to extend the deadline to 10 July.

That means there’s still time to apply for our @embo.org course at meetings.embo.org/event/25-bio... !!

Speakers: @amjjbonvin.bsky.social @bioinfo.se @brianjimenez @dinaSchneidman @ezgikaraca.bsky.social @lindorfflarsen.bsky.social @matthieumontes.bsky.social @marclensink.bsky.social @oraSchueler-Furman @raphaelGuerois @sokrypton.org @birtheKragelund @alessandraVilla

Only a few days left to apply for our EMBO course with a great lineup of speakers and tutors! Please feel free to RT!

Course website: meetings.embo.org/event/25-bio...

Organizers: myself, @amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social

Location: www.ibg.edu.tr

Also, many thanks to @amjjbonvin.bsky.social & HADDOCK Team for including PROT-ON in their HADDOCK2.4 Antibody-Antigen tutorial!

If you are looking for a real case application example of PROT-ON, you can check: www.bonvinlab.org/education/HA...

1 year ago, we launched PROT-ON to help scientists scan and understand mutations across protein-protein interfaces.

Since then, it has been used by researchers from all around the world!

If you haven’t tried PROT-ON yet, here is the link to our web resource: proton.tools.ibg.edu.tr:8001/about

Thanks a lot for highlighting our work!! 💚💚

Today is the last day to register for the CSSB Symposium!

www.cssb-hamburg.de/symposium2025

@carobarisch.bsky.social @topf-lab.bsky.social @bosse-lab.bsky.social @landaulabcssb.bsky.social @jankosinski.bsky.social @ezgikaraca.bsky.social @jpoverington.bsky.social @marylynaddo.bsky.social

Ezgi Karaca @ezgikaraca.bsky.social from the Izmir Biomedicine and Genome Center will give a talk during the Emerging Themes session of our symposium.

Register: cssb-hamburg.de/symposium2025

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

🥹🍀🥹🍀

Very much looking forward to the 25th anniversary symposium of ChemBioChem and ChemPhysChem #CBCCPC2025 in Berlin on October 23rd and 24th, 2025.

There is an ever growing list of amazing speakers confirmed for this event. (1/2)

#chemsky #ChemBio @chemistryeurope.bsky.social

www.cbc-cpc2025.org

TUBITAK 2509 call - France-Turkey bilateral research program

I'm so happy to learn that our Turkey-France joint project application with @marclensink.bsky.social has been accepted!

This funding will allow us to explore whether we can sample meaningful protein interaction dynamics with MassiveFold.

Excited to be "officially" collaborating with Marc again! ♥️

Inspired by Wallner's AFsample approach, @busrasavas.bsky.social's MinnieFold produced good quality antibody-antigen models even with 95% reduced sampling over CAPRI55 targets.

Just accepted in Proteins!

Paper: www.biorxiv.org/content/10.1...
Github: github.com/CSB-KaracaLa...

We offer an amazing and timely program, spanning integrative modeling, AI-based protein/complex modeling, and biomolecular dynamics.

There are also several fellowship options!

Looking forward to host this year's fun during 28 September – 03 October 2025 in Izmir 🌴

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

Maybe this one?
Predicting multiple conformations of ligand binding sites in proteins suggests that AlphaFold2 may remember too much
www.pnas.org/doi/abs/10.1...

😍🙌

Congrats Nessim 👏👏

😂😂😂

Today is the #HADDOCK day - lectures and tutorials running hot to melt the snow!

... Here, we unmasked the input sequence and sidechains. The outcome was chosen as our best model.

... "V1, dropout, no templates, recycles 21, seed 4, paired MSA" (rank 3).

2) We then energy-minimized the top model with HADDOCK (due to system updates, ColabFold's refinement option was not working then)

3) We used AF2Rank (4 recycles) to get the pLDDT score of the HADDOCK-refined model...

1) We ran a mini version of Wallner's aggressive sampling by generating 20 models (4 per network) for each sampling parameter. We extended the approach by including AF2.3 in the sampling and playing with the MSA pairing.

As an outcome, the best pLDDT of the peptide was obtained with ....

Super proud to have been listed as one of the successful groups in predicting the structure of an antibody-peptide during @capridock.bsky.social's 55th round! This was our first attempt in CAPRI as the Karaca team with @busrasavas.bsky.social @iremylmazbilek.bsky.social @atakanozsan 💪

Thank you for your contributions, Marc!! 😊🍀

These messages became the great surprise of today, thanks to the fact that I was “just a bit” late to check the notifications in my Bluesky app😅😍