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Büşra Savaş

@busrasavas.bsky.social

PhD student IBG & DEU | Computational Structural Biologist

16 Posts52 Follower75 Folgt
Ezgi Karaca@ezgikaraca.bsky.social · 4mo ago

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

Büşra Savaş@busrasavas.bsky.social · 6mo ago

🚀 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 👇

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👇

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? 🧬✨

Communications Biology@commsbio.nature.com · 12mo ago

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...

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

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👇

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👇

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps https://www.biorxiv.org/content/10.1101/2025.07.25.666757v1

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

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!

Itai Yanai@itaiyanai.bsky.social · last yr.

We had two great 'Night Science' workshops on the creative scientific process in Heidelberg yesterday (at EMBL and at the EMBO PhD Course). Here are the slides if you're interested in running something like this at your place! docs.google.com/presentation...

Greenlab Zürich@greenlabzh.bsky.social · last yr.

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

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

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...