Ezgi Karaca
@ezgikaraca.bsky.social
Research Group Leader @ Izmir Biomedicine and Genome Center & DEU, TR | CASP14-15 Assembly Assessor | Computational Structural Biologist
Pinned
Ezgi Karaca
@ezgikaraca.bsky.social
· Aug 22
🚀 Excited to share that our article with @ezgikaraca.bsky.social is now published in Communications Biology!
In this study, we explored DNA readout rules of almost identical DNMT3A and DNMT3B (91% sequence similarity!), and we asked: how can nearly the same proteins “see” DNA so differently? 🧬✨
In this study, we explored DNA readout rules of almost identical DNMT3A and DNMT3B (91% sequence similarity!), and we asked: how can nearly the same proteins “see” DNA so differently? 🧬✨
Comparative dynamics analysis identifies key residues driving sequence specificity differences between human DNA methyltransferases DNMT3A and DNMT3B.
@aysebercinb.bsky.social
@ezgikaraca.bsky.social
www.nature.com/articles/s42...
@aysebercinb.bsky.social
@ezgikaraca.bsky.social
www.nature.com/articles/s42...
Main PhD work, as well as the first first-author paper of @aysebercinb.bsky.social , where we investigate how two nearly identical enzymes target different substrates!!
For more, please 👇
For more, please 👇
😍😊🍀
Interesting talk by @ezgikaraca.bsky.social at #ChemBioPhys2025. She talked about the use of AI for predictions of protein structures with a lot of exciting insights into the CASP competition and into the prediction of protein-protein interactions. www.biorxiv.org/content/10.1...
October 24, 2025 at 3:32 PM
😍😊🍀
Reposted by Ezgi Karaca
It was a huge pleasure to host the morning session of #ChemBioPhys2025. A huge thank you to the speakers @gassergroup.bsky.social, Harald Schwalbe, @ezgikaraca.bsky.social, Stephen Kent, Joseph Braymer, Hsuan-Ai Chen, @borisvauzeilles.bsky.social and @romanrenger.bsky.social. I learned a lot!
October 24, 2025 at 12:06 PM
It was a huge pleasure to host the morning session of #ChemBioPhys2025. A huge thank you to the speakers @gassergroup.bsky.social, Harald Schwalbe, @ezgikaraca.bsky.social, Stephen Kent, Joseph Braymer, Hsuan-Ai Chen, @borisvauzeilles.bsky.social and @romanrenger.bsky.social. I learned a lot!
🥹😍🥰thank you for this beautiful post!
Just wrapped up the EMBO Integrative Modeling Course, beautifully organized by @ezgikaraca.bsky.social & her amazing team with care🩵! From protein docking & AI-based modeling to endless coffee breaks,seaside dinners, and karaoke, it was science + community at its best. Truly unforgettable @embo.org
And the legacy continues! 😊
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
October 8, 2025 at 7:05 PM
🥹😍🥰thank you for this beautiful post!
And the legacy continues! 😊
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
October 6, 2025 at 1:13 PM
And the legacy continues! 😊
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
Reposted by Ezgi Karaca
Traveling to beautiful Izmir tomorrow for the EMBO meeting on modeling biomolecules interactions, where I will present the CAPRI blind prediction experiment on Tuesday. Looking forward to it. Thanks to @ezgikaraca.bsky.social and other organizers for the invitation
meetings.embo.org/event/25-bio...
meetings.embo.org/event/25-bio...
Integrative modelling of biomolecular interactions
Experimental structural studies of interactions can be costly, low-throughput, and challenging. Therefore, computational methods aiming to model protein complexes are particularly valuable. The accur…
meetings.embo.org
September 28, 2025 at 9:04 PM
Looking forward hosting you here and listening to your awesome work!! 😍
Going to Izmir for the meetings.embo.org/event/25-bio...
I will talk on monday about interactive molecular visualization and simulation methods! See you there!
Thanks to the organizers for the invitation! @ezgikaraca.bsky.social @amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social
I will talk on monday about interactive molecular visualization and simulation methods! See you there!
Thanks to the organizers for the invitation! @ezgikaraca.bsky.social @amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social
Integrative modelling of biomolecular interactions
Experimental structural studies of interactions can be costly, low-throughput, and challenging. Therefore, computational methods aiming to model protein complexes are particularly valuable. The accur…
meetings.embo.org
September 27, 2025 at 8:53 AM
Looking forward hosting you here and listening to your awesome work!! 😍
Main PhD work, as well as the first first-author paper of @aysebercinb.bsky.social , where we investigate how two nearly identical enzymes target different substrates!!
For more, please 👇
For more, please 👇
🚀 Excited to share that our article with @ezgikaraca.bsky.social is now published in Communications Biology!
In this study, we explored DNA readout rules of almost identical DNMT3A and DNMT3B (91% sequence similarity!), and we asked: how can nearly the same proteins “see” DNA so differently? 🧬✨
In this study, we explored DNA readout rules of almost identical DNMT3A and DNMT3B (91% sequence similarity!), and we asked: how can nearly the same proteins “see” DNA so differently? 🧬✨
Comparative dynamics analysis identifies key residues driving sequence specificity differences between human DNA methyltransferases DNMT3A and DNMT3B.
@aysebercinb.bsky.social
@ezgikaraca.bsky.social
www.nature.com/articles/s42...
@aysebercinb.bsky.social
@ezgikaraca.bsky.social
www.nature.com/articles/s42...
August 22, 2025 at 11:21 AM
Main PhD work, as well as the first first-author paper of @aysebercinb.bsky.social , where we investigate how two nearly identical enzymes target different substrates!!
For more, please 👇
For more, please 👇
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...
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...
July 29, 2025 at 1:01 PM
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...
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...
Reposted by Ezgi Karaca
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
cbc-cpc2025.org
October 23-24, 2025, Berlin
Please like and share! #ChemBioPhys2025
July 1, 2025 at 3:21 PM
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
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... !!
That means there’s still time to apply for our @embo.org course at meetings.embo.org/event/25-bio... !!
June 17, 2025 at 1:29 PM
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... !!
That means there’s still time to apply for our @embo.org course at meetings.embo.org/event/25-bio... !!
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
Course website: meetings.embo.org/event/25-bio...
Organizers: myself, @amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social
Location: www.ibg.edu.tr
June 11, 2025 at 8:48 AM
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
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...
If you are looking for a real case application example of PROT-ON, you can check: www.bonvinlab.org/education/HA...
May 13, 2025 at 6:56 AM
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...
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
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
May 13, 2025 at 6:54 AM
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
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
Reposted by Ezgi Karaca
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
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
April 15, 2025 at 9:26 AM
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
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
Reposted by Ezgi Karaca
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
Register: cssb-hamburg.de/symposium2025
@carobarisch.bsky.social @bosse-lab.bsky.social @landaulabcssb.bsky.social @jankosinski.bsky.social
March 31, 2025 at 1:30 PM
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
Register: cssb-hamburg.de/symposium2025
@carobarisch.bsky.social @bosse-lab.bsky.social @landaulabcssb.bsky.social @jankosinski.bsky.social
Reposted by Ezgi Karaca
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
There is an ever growing list of amazing speakers confirmed for this event. (1/2)
#chemsky #ChemBio @chemistryeurope.bsky.social
www.cbc-cpc2025.org
March 3, 2025 at 1:57 PM
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
There is an ever growing list of amazing speakers confirmed for this event. (1/2)
#chemsky #ChemBio @chemistryeurope.bsky.social
www.cbc-cpc2025.org
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! ♥️
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! ♥️
February 24, 2025 at 9:57 AM
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! ♥️
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...
Just accepted in Proteins!
Paper: www.biorxiv.org/content/10.1...
Github: github.com/CSB-KaracaLa...
February 22, 2025 at 10:38 AM
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...
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 🌴
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
Organized by myself & @amjjbonvin.bsky.social & @arneelof.bsky.social & @lindorfflarsen.bsky.social
January 2, 2025 at 9:01 AM
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 🌴
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
Organized by myself & @amjjbonvin.bsky.social & @arneelof.bsky.social & @lindorfflarsen.bsky.social
January 2, 2025 at 8:57 AM
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
Organized by myself & @amjjbonvin.bsky.social & @arneelof.bsky.social & @lindorfflarsen.bsky.social
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 💪
January 13, 2024 at 9:21 AM
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 💪