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Max Bonomi

@bonomimax.bsky.social

Head of Computational Structural Biology Lab @pasteur.fr. ERC-CoG 2022. Research Director DR2 @cnrs.bsky.social. Founder/developer @plumed.org

41 Posts1565 Follower2817 Folgt
Max Bonomi@bonomimax.bsky.social · 2w ago

Fantastic opportunity at @pasteur.fr in Spyros’ brand new lab, especially if you like protein design 🎉

Antigen Evolution & Design Lab@antigenevo.bsky.social · 2w ago

🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st

Max Bonomi@bonomimax.bsky.social · 5mo ago

📣 Excited to co-organize this @embo.org Lecture Course - #AI driven approaches in structural biology 📅 26 April - 2 May 2026 in Bengalore (India). More info and registration below @pasteur.fr @cnrsbiologie.bsky.social meetings.embo.org/event/26-ai-...

AI-driven approaches in structural biology

Recent breakthroughs in artificial intelligence have transformed structural biology, enabling accurate protein structure prediction and de novo design at unprecedented scale. This EMBO Lecture Course…

meetings.embo.org

Max Bonomi@bonomimax.bsky.social · 9mo ago

Don’t miss this opportunity to work with a fantastic mentor, a great team, in a beautiful city of France!

Center for Structural Biology (CBS Montpellier)@cbsmontpellier.bsky.social · 9mo ago

Postdoctoral position in the team of Alessandro Barducci in the CBS, focusing on multiscale simulations of RNA-driven condensates, with applications in synthetic biology. More information : www.cbs.cnrs.fr/images/jobs/... The position is expected to start in early 2026, with some flexibility.

Bussi Lab@bussilab.org · 9mo ago

A new tutorial manuscript is out! 🚀 Making @plumed.org fly: a tutorial on optimizing performance, by Daniele Rapetti, @bonomimax.bsky.social @carlocamilloni.bsky.social @bussigio.bsky.social and Gareth Tribello. arxiv.org/abs/2511.02699

Making PLUMED fly: a tutorial on optimizing performance

PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. Whi...

arxiv.org

Max Bonomi@bonomimax.bsky.social · 9mo ago

See you in Toulouse for this exciting @cecamevents.bsky.social workshop! #cryoEM #cryoET #AI #modeling

Matthieu Chavent@matthchavent.bsky.social · 9mo ago

🔬 CECAM Workshop: “Integrative and Multiscale Modelling Approaches to Illuminate CryoEM/ET Data” Join us in Toulouse, 24–26 March 2026, to explore how molecular simulations, AI tools, can be integrated to cryo-EM and cryo-ET data. 🧬 Selection: brief CV + motivation letter required. Apply 👇

Paul Robustelli@paulrobustelli.bsky.social · 10mo ago

Our work developing a maximum entropy reweighting method to refine all-atom ensembles of IDPs with extensive NMR and SAXS datasets is now out in @natcomms.nature.com: rdcu.be/eKlK7 Led by @dartmouthchem.bsky.social graduate student Kaushilk Borthakur in collaboration with @bonomimax.bsky.social

Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution

Nature Communications - This study demonstrates how to combine molecular dynamics computer simulations with experimental biophysical data to determine accurate atomic-resolution ensembles of...

rdcu.be

Max Bonomi@bonomimax.bsky.social · last yr.

❄️ Even high-resolution #cryoEM maps can still hide a few secrets 🔍 Discover how we uncover them in this exciting collaboration with @egreene.bsky.social @fraserlab.com @pasteur.fr @cnrsbiologie.bsky.social 📄 Preprint: www.biorxiv.org/content/10.1...

Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity

To maintain metabolic homeostasis, enzymes must adapt to fluctuating nutrient levels through mechanisms beyond gene expression. Here, we demonstrate that human glutamine synthetase (GS) can reversibly polymerize into filaments aided by a composite binding site formed at the filament interface by the product, glutamine. Time-resolved cryo-electron microscopy (cryo-EM) confirms that glutamine binding stabilizes these filaments, which in turn exhibit reduced catalytic specificity for ammonia at physiological concentrations. This inhibition appears induced by a conformational change that remodulates the active site loop ensemble gating substrate entry. Metadynamics ensemble refinement revealed >10 Å conformational range for the active site loop and that the loop is stabilized by transient contacts. This disorder is significant, as we show that the transient contacts which stabilize this loop in a closed conformation are essential for catalysis both in vitro and in cells. We propose that GS filament formation constitutes a negative-feedback mechanism, directly linking product concentration to the structural and functional remodeling of the enzyme. ### Competing Interest Statement HY is an employee of JSR. J.S.F. is a consultant to, a shareholder of, and receives sponsored research support from Relay Therapeutics. National Institutes of Health, https://ror.org/01cwqze88, F32GM144982, R35GM145238

biorxiv.org

Max Bonomi@bonomimax.bsky.social · last yr.

AlphaFold’s success builds on decades of tech advances, massive efforts to collect, curate, and share structural data, and rigorous benchmarking. What will it take to see a similar leap in structural ensemble prediction? @stephanieaw.bsky.social and I share some thoughts here 👇 Feedback is welcome!

Stephanie Wankowicz@stephanieaw.bsky.social · last yr.

Predicting macromolecular ensembles is incredibly promising. However, as no single experimental method can map a conformational ensemble’s full atomistic landscape, there are foundational questions: What exactly are we trying to predict, and how will we know when we have succeeded?