iiinova — where your digital self keeps evolving

Büşra Savaş @busrasavas.bsky.social · 21/09/2026

I’m currently looking for postdoctoral opportunities where I can keep learning, exploring, and, most importantly, keep that curiosity spark alive. ✨ Here’s to new questions, new places, and new adventures!💚

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Büşra Savaş @busrasavas.bsky.social · 21/09/2026

• Collaborated with enthusiastic researchers to assist in addressing diverse biological questions, from understanding how structural changes affect function to exploring protein function through computational modeling (Circir et al., 2021; Özden-Yılmaz et al., 2023; Turan et al., 2024).

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Büşra Savaş @busrasavas.bsky.social · 21/09/2026

• In CAPRI61, the AF2Rank-PPI approach, together with an updated composite score, ranked as the top-scorer approach in the scoring category, successfully identifying high- and medium-quality antibody-antigen predictions among the decoy sets.

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Büşra Savaş @busrasavas.bsky.social · 21/09/2026

• Participated in two CAPRI rounds (55th and 61st). In CAPRI55, MinnieFold ranked among the top-performing approaches in the sampling category (Savas et al., Proteins, 2025).

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Büşra Savaş @busrasavas.bsky.social · 21/09/2026

• Benchmarked the performance of AlphaFold for evaluating NMR-derived interactions by extending the existing AF2Rank framework to AF2Rank-PPI (unpublished work, available as part of the thesis).

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Büşra Savaş @busrasavas.bsky.social · 21/09/2026

• Explored how binding-induced conformational changes can be detected through distance distributions encoded in AlphaFold distograms (Savas et al., FEBS Letters, 2026).

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Büşra Savaş @busrasavas.bsky.social · 21/09/2026

Through challenges, countless questions, and probably an unreasonable amount of coffee, here’s a brief summary of my PhD journey: • Developed MinnieFold, an efficient and greener pipeline for protein complex modeling (Savas et al., Proteins, 2025).

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Büşra Savaş @busrasavas.bsky.social · 21/09/2026

I’m incredibly grateful to have worked with @ezgikaraca.bsky.social , who not only supported me throughout this journey but also guided me through both science and life. I will always cherish the time we spent researching and learning together 🫶

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Büşra Savaş @busrasavas.bsky.social · 21/09/2026

Some news taste better after a little marination 🎓 After a reviving summer, I’m happy to finally share that I’ve successfully defended my PhD in late March!

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Ezgi Karaca @ezgikaraca.bsky.social · 27/03/2026

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!

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BioExcel CoE @bioexcelcoe.bsky.social · 18/03/2026

Join us in a couple of weeks to hear @ezgikaraca.bsky.social talk about "DynaPIN: a tool for characterising dynamic protein interfaces" 🗓️ 31 March 2026, 15:00 CET ✍️ bioexcel.eu/lgmq #webinar #ComputerSimulation #protein #molecularmodeling

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Büşra Savaş @busrasavas.bsky.social · 09/02/2026

Full story of “Exploring the potential of AlphaFold distograms for predicting binding‐induced hinge motions” in 👉 lnkd.in/dkUrBh4E Check out our GitHub repo to get your hands on the data and code: lnkd.in/daSREaGG

lnkd.in

This link will take you to a page that’s not on LinkedIn

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Büşra Savaş @busrasavas.bsky.social · 09/02/2026

🌟 Here, we proudly present the first systematic benchmark analysis of AlphaFold distograms across all available versions, demonstrating that distograms may encode a more fundamental layer of conformational information than what is captured by the predicted output structures.

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Büşra Savaş @busrasavas.bsky.social · 09/02/2026

Beyond AF2-based methods, we analyzed the effect of MSA alterations in AF3 using AF3sample2 and AF3_cluster. We further investigated how distograms translate into structural ensembles, comparing AF-based ensembles against generative approaches including BioEmu, Chai-1, and Boltz-2.

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Büşra Savaş @busrasavas.bsky.social · 09/02/2026

Following up on our preprint: We have extended our distogram analysis to three additional proteins with varying structural contexts: MIA40, IL1R1 and EIF2B3. For all, we identified residue pairs indicative of hinge-like motions through bimodal distogram peaks.

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Büşra Savaş @busrasavas.bsky.social · 09/02/2026

Since its first version at CASP13, AlphaFold uses distance probability distributions aka distograms to guide the structural modeling. Here, in this perspective, we have shown that distograms may offer rapid, structure-free, binding induced hinge motion detection.

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Büşra Savaş @busrasavas.bsky.social · 09/02/2026

🚀 Excited to announce that our perspective piece with @ezgikaraca.bsky.social and @aysebercinb.bsky.social on AlphaFold distograms is now published in @febsletters.bsky.social!! Here is what we did further 👇

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Büşra Savaş @busrasavas.bsky.social · 11/12/2025

364 days a year we use AlphaFold to predict protein structure… But not on Christmas Eve! That’s when Santa does the predictions. But beware, computational structural biologists on the naughty list will only get low pLDDTs #SantaFold #bananapro

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A. Berçin Barlas @aysebercinb.bsky.social · 22/08/2025

🚀 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? 🧬✨

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Ezgi Karaca @ezgikaraca.bsky.social · 29/07/2025

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...

biorxiv.org

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...

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Büşra Savaş @busrasavas.bsky.social · 29/07/2025

Taken together, our results point to new exciting directions for structural biology through distograms: - Rapid flexibility detection - Improved EM map interpretation - Distogram-informed ensemble modeling Full story 👉 doi.org/10.1101/2025... 💻 GitHub: github.com/CSB-KaracaLa...

github.com

GitHub - CSB-KaracaLab/af-distogram-flexibility: Data accompanying our paper entitled "Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps "

Data accompanying our paper entitled "Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps " - CSB-KaracaLab/af-distogram-flexibility

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Büşra Savaş @busrasavas.bsky.social · 29/07/2025

We next asked: how do AF2-based sampling strategies affect distograms? We tested MinnieFold, AFsample2, and AF_cluster. The biggest impact came from the AF2 version itself. Only AF2.3 mirrored AF3’s flexibility-aware distogram profile.

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Büşra Savaş @busrasavas.bsky.social · 29/07/2025

We run MD of apo and holo AK2 and revealed that holo AK2 hinge distance is sampled rarely in its apo state! Strikingly, apo AF3 distogram reproduces the exact same behavior!!🤯

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Büşra Savaş @busrasavas.bsky.social · 29/07/2025

Surprisingly, AF3 apo and holo AK2 predictions beautifully reflect this conformational change, where C-ter of AK2 experiences a disorder-to-order transition upon beta-stacking itself to AIFM1👇 To track hinge motion, we concentrated on 230-233 CB–CB distances of AK2.

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Büşra Savaş @busrasavas.bsky.social · 29/07/2025

We tested this hypothesis on AK2:AIFM1 complex, a molecular switch between energy metabolism and cell death. 🔁💀 Its function depends on a hinge-driven motion, that is: ✔Recently revealed by two cryo-EM maps ✔ Occurs upon binding ❌Not seen in crystal structures

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Büşra Savaş @busrasavas.bsky.social · 29/07/2025

A primer on distograms: for each residue pair, AF outputs distance probability distributions. Earlier, it was shown that the shape of the distogram peaks may inform us on protein flexibility. How? ✔ Unimodal peak → rigid behavior ✔ Bimodal peak → flexible behavior

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Büşra Savaş @busrasavas.bsky.social · 29/07/2025

🚨 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👇

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Alexandre Bonvin @amjjbonvin.bsky.social · 29/07/2025

A small reminder to all structural biologists around working on biomolecular complexes: please consider sharing your complexes as targets for CAPRI - AI has not solved all structure prediction problems and there are still challenges! See www.capri-docking.org/contribute/

capri-docking.org

CAPRI Docking

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Ezgi Karaca @ezgikaraca.bsky.social · 11/06/2025

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

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Büşra Savaş @busrasavas.bsky.social · 22/05/2025

We want awe. We want discovery. And we want them now! Huge thanks to Itai and Martin for the most enjoyable lecture on Night Science — a reminder that opennes lie at the heart of discovery!

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Greenlab Zürich @greenlabzh.bsky.social · 06/05/2025

This week's #SustainableTipTuesday is about computation - did you know there is a version of AlphaFold that uses 95% less energy than the regular version? Take a look below💡 #greenlabs

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Ezgi Karaca @ezgikaraca.bsky.social · 22/02/2025

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...

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Ezgi Karaca @ezgikaraca.bsky.social · 02/01/2025

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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Ezgi Karaca @ezgikaraca.bsky.social · 13/01/2024

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 💪

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