Aaand one more good news for the Bioexcel enthusiasts, preferentially living in Greece or Türkiye!

BioExcel CoE@bioexcelcoe.bsky.social · 4w ago

Registration is open for our 6th Ambassador Program hands-on #workshop focused on the use of #GROMACS, #HADDOCK and #BioBB 🗓️ 18-20 November 2026 🌍 Athens, Greece Info & registration ➡️ bioexcel.eu/a9nq @ezgikaraca.bsky.social #ComputerSimulation #moleculardynamics #integrativemodelling #workflows

Our new tool to analyze protein interfaces from MD trajectories is out in JMB, in its Computational Resources Special Issue! 🍀 Our tool, DynaPIN can be used to understand the biology of binding at the atomistic scale, as we have showed in its paper at doi.org/10.1016/j.jm... For more details👇👇👇

A. Berçin Barlas@aysebercinb.bsky.social · 3w ago

🎉 Finally out!! Our paper, "DynaPIN: A tool for characterizing dynamic protein interfaces" is accepted in JMB! @ezgikaraca.bsky.social (in collaboration with @sacquin-mo.eurosky.social & co.) DynaPIN is an open-source pipeline for analyzing dynamic protein interfaces. 🧵👇 📄 doi.org/10.1016/j.jm...

Our rescheduled webinar "DynaPIN: a tool for characterising dynamic protein interfaces" is happening tomorrow! 🗓️ 28 April 2026, 15:00 CET ✍️ bioexcel.eu/lgmq @ezgikaraca.bsky.social #webinar #ComputerSimulation #protein #molecularmodeling

Webinar: DynaPIN: A Tool for Characterizing Dynamic Protein Interfaces (2026-04-28)

Date: 28 April 2026 Time: 15:00 CET Registration Abstract Static structural models often fail to capture the dynamic mechanisms of protein interactions. To address this, we introduce DynaPIN, an open...

bioexcel.eu

Navigating the pre- and post-AlphaFold divide: CAPRI 8th evaluation meeting www.authorea.com/users/348903...

Navigating the Pre- and Post-AlphaFold Divide: CAPRI 8th evaluation meeting, February 12-14, Grenoble, FR

Navigating the Pre- and Post-AlphaFold Divide: CAPRI 8th evaluation meeting, February 12-14, Grenoble, FRAlexandre M.J.J. Bonvin1 and M. F. Lensink21 Bijvoet Centre for Biomolecular Research, Faculty ...

authorea.com

Only a couple of days left to introduce our brand new tool, DynaPIN that @aysebercinb.bsky.social developed (in collaboration with @sacquin-mo.bsky.social & co.) to analyze dynamic/ensemble protein interfaces!

BioExcel CoE@bioexcelcoe.bsky.social · 4mo ago

🎗️ reminder that our #webinar on characterising dynamic #protein interfaces with the DynaPIN #software will take place next week; 🗓️ 31 March 2026, 15:00 CET ✍️ bioexcel.eu/lgmq @ezgikaraca.bsky.social #webinar #ComputerSimulation #protein #molecularmodeling

😍😊🍀

Stephan Hacker@stephanhacker2.bsky.social · 10mo ago

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...

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!

Debangana Moitra@debanganamoitra.bsky.social · 10mo ago

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 ! 🍀🧿

Ezgi Karaca@ezgikaraca.bsky.social · 2y ago

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

And we're off

Our pleasure, Marc! Let the #EmboIntegMod25 begin! 🤩

Marc Lensink@marclensink.bsky.social · 10mo ago

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...

Looking forward hosting you here and listening to your awesome work!! 😍

Matthieu Montes@matthieumontes.bsky.social · 10mo ago

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

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 👇

A. Berçin Barlas@aysebercinb.bsky.social · 12mo ago

🚀 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? 🧬✨

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...

Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps

AlphaFold (AF) models are widely used in cryo-EM workflows, but their static structure predictions limit the interpretation of flexible or unresolved regions. To address this, we investigate whether A...

biorxiv.org

Büşra Savaş@busrasavas.bsky.social · last yr.

🚨 Super excited for our new preprint on flexibility cues in AlphaFold! Together with @ezgikaraca.bsky.social and @aysebercinb.bsky.social, we found that distograms of AF2.3 and AF3 mirror MD sampling by predicting the extent of a novel conformational change! 🤯 For more👇

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... !!

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

Ezgi Karaca@ezgikaraca.bsky.social · last yr.

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

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...

HADDOCK2.4 basic Antibody - Antigen tutorial including a comparison with AlphaFold

A small tutorial on predicting with HADDOCK a protein-protein complex using interface residues identified from NMR chemical shift perturbation experiments and comparing the results with predictions fr...

bonvinlab.org

Ezgi Karaca@ezgikaraca.bsky.social · last yr.

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

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

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

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 🌴

Ezgi Karaca@ezgikaraca.bsky.social · 2y ago

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

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

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

Arjen Jakobi@cryotud.bsky.social · 2y ago

Really looking forward to welcoming & meeting the participants of our #EMBOStructBio course this morning! Many of our speakers/tutors are here: @moalquraishi.bsky.social @sykhalid.bsky.social @ezgikaraca.bsky.social @amjjbonvin.bsky.social @gchojnowski.bsky.social @drmelissagraewert.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 💪