Sign in

Max Bonomi

@bonomimax.bsky.social
1.6K followers 2.8K following 41 posts

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

PostsRepliesMedia
Max Bonomi @bonomimax.bsky.social · 22/07/2026
Fantastic opportunity at @pasteur.fr in Spyros’ brand new lab, especially if you like protein design 🎉
0105
Max Bonomi @bonomimax.bsky.social · 01/05/2026
Last day of this fantastic @embo.org lecture course ‘AI-driven approaches in structural biology’ in Bengaluru, India @pasteur.fr @cnrsbiologie.bsky.social
0151
Reposted by Max Bonomi
Bussi Lab @bussilab.org · 09/04/2026
Want to contribute to a major #opensource project for molecular simulations? We’re opening a research technologist position at SISSA (Trieste) to work on @plumed.org (scientific coding / #HPC) within the #RNAScale project. Fill the expression of interest form: www.bussilab.org/rnascale #joinus
bussilab.org
RNAScale
Exploring RNA Dynamics across Scales
072
Reposted by Max Bonomi
Matthieu Chavent @matthchavent.bsky.social · 17/03/2026
Looking forward welcoming next week all the participants of the CECAM workshop organized with @sonyahanson.bsky.social , Celia Plisson-Chastang, and @bonomimax.bsky.social at the Museum of Toulouse Full program: www.cecam.org/workshop-det...
093
Max Bonomi @bonomimax.bsky.social · 25/02/2026
📣 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-...
meetings.embo.org
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…
0156
Max Bonomi @bonomimax.bsky.social · 03/02/2026
and for refining AF2 models for small molecules virtual screenings www.biorxiv.org/content/10.1...
biorxiv.org
020
Max Bonomi @bonomimax.bsky.social · 03/02/2026
This work follows our previous exploration of AF2 distograms for generating accurate, atomistic ensembles of Intrinsically Disordered Proteins www.biorxiv.org/content/10.1...
biorxiv.org
110
Max Bonomi @bonomimax.bsky.social · 03/02/2026
✨ New preprint by Nicolas Portal in collaboration with @vincentmallet.bsky.social 🚀 We incorporate AF2 distograms in #ML protein representations for prediction of ligand binding sites & affinity + protein stability + various RNA properties @pasteur.fr @erc.europa.eu www.biorxiv.org/content/10.6...
biorxiv.org
1174
Max Bonomi @bonomimax.bsky.social · 28/11/2025
Amazing opportunity!
060
Max Bonomi @bonomimax.bsky.social · 07/11/2025
Don’t miss this opportunity to work with a fantastic mentor, a great team, in a beautiful city of France!
094
Reposted by Max Bonomi
Bussi Lab @bussilab.org · 05/11/2025
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
arxiv.org
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...
194
Max Bonomi @bonomimax.bsky.social · 01/11/2025
See you in Toulouse for this exciting @cecamevents.bsky.social workshop! #cryoEM #cryoET #AI #modeling
070
Reposted by Max Bonomi
Paul Robustelli @paulrobustelli.bsky.social · 10/10/2025
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
rdcu.be
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...
3247
Max Bonomi @bonomimax.bsky.social · 07/07/2025
Yep I think this also is feasible!
020
Max Bonomi @bonomimax.bsky.social · 07/07/2025
Ahah I thought you were commenting on the other bioRxiv. My fault. In any case, the answer is yes!
110
Max Bonomi @bonomimax.bsky.social · 07/07/2025
Yes, if some low res density is actually there. Same for semi-ordered waters, lipids or glycans 🎉
310
Max Bonomi @bonomimax.bsky.social · 07/07/2025
❄️ 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...
biorxiv.org
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
0206
Max Bonomi @bonomimax.bsky.social · 23/06/2025
Any sticker left for a colleague? 😜
110
Max Bonomi @bonomimax.bsky.social · 21/06/2025
🔧 Try it now with the dev version of @plumed.org 📂 Reproducibility: www.plumed-nest.org/eggs/25/014 📚 Tutorial (coming soon): www.plumed-tutorials.org
040
Max Bonomi @bonomimax.bsky.social · 21/06/2025
🚀 Super excited to share our new work, led by @vschnapka.bsky.social bAIes, a Bayesian framework for generating accurate atomic-resolution ensembles of IDPs using #AlphaFold info! Now on @biorxivpreprint.bsky.social → feedback welcome! @pasteur.fr @erc.europa.eu www.biorxiv.org/content/10.1...
biorxiv.org
33810
Max Bonomi @bonomimax.bsky.social · 27/05/2025
Exciting symposium coming soon in Grenoble!
081
Reposted by Max Bonomi
Bussi Lab @bussilab.org · 16/05/2025
Our integrative approach using #MD and #cryoEM data to construct structural ensembles of #RNA just published on @natcomms.bsky.social doi.org/10.1038/s414... Lead by Elisa Posani, with @magistratolab.bsky.social @bonomimax.bsky.social @pjanos.bsky.social @navtejtoor.bsky.social and Daniel Haack 🎉
0268
Reposted by Max Bonomi
PSB_Grenoble @psb-grenoble.bsky.social · 09/05/2025
🧬PSB Symposium on " #MachineLearning in Cellular #StructuralBiology ", EPN Campus Grenoble, France, 26-27 June 2025🧬 📢Reminder - Call for abstracts (posters & short talks) Submission & registration deadline 25 May: www.psb-grenoble.eu/psbsymposium... @esrf.fr @embl.org @illneutrons.bsky.social
174
Max Bonomi @bonomimax.bsky.social · 07/05/2025
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!
1215
Max Bonomi @bonomimax.bsky.social · 19/03/2025
Last session is about "Ethics and AI", with a fantastic lecture from Julie Allouche @pasteur.fr and Pierre Noro @pierrenoro.bsky.social @sciencespo.bsky.social
050
Max Bonomi @bonomimax.bsky.social · 19/03/2025
Next is technical challenges related to developing/using AI with Youssef Ghorbal and Thomas Menard
130
Max Bonomi @bonomimax.bsky.social · 19/03/2025
Last day of our "AI for Life Sciences" course @pasteuredu.bsky.social This morning we talk about Intellectual Property & AI with Nicolas Torno and Helene Chommy from DARRI @pasteur.fr
1193
Max Bonomi @bonomimax.bsky.social · 18/03/2025
Final thematic session of our "AI for Life Sciences" is "AI in Neuroscience" with Jean-Baptiste Masson @pasteur.fr @pasteuredu.bsky.social
1131
Max Bonomi @bonomimax.bsky.social · 18/03/2025
It is now time for "AI in Structural Biology" with Guillaume Bouvier: AlphaFold and beyond! Short talks by @bardiauxb.bsky.social Ludovic Sauguet Vincent Schnapka and @duyvd.bsky.social @pasteur.fr @pasteuredu.bsky.social
0196
Reposted by Max Bonomi
Laura Cantini @cantinilab.bsky.social · 18/03/2025
AI for life sciences day 2 started! @m-albert.bsky.social is now teaching AI for image analysis. Felipe Llinares from Bioptimus will then talk about LLMs, with short talks from @jkobject.com from my team and @emordret.bsky.social from @audeber.bsky.social team. @pasteur.fr @pasteuredu.bsky.social
0167
Max Bonomi @bonomimax.bsky.social · 17/03/2025
We are back with our "AI for life sciences" course @pasteur.fr @pasteuredu.bsky.social with a deep dive into Neural Networks with @vincentmallet.bsky.social
1203
Reposted by Max Bonomi
Laura Cantini @cantinilab.bsky.social · 17/03/2025
📢Here WE go!!! AI for life sciences course kicking off at @pasteur.fr with a lecture from @laineelodie.bsky.social. Happy to see so many students on campus interested in AI! @bonomimax.bsky.social @pasteuredu.bsky.social
0195
Max Bonomi @bonomimax.bsky.social · 05/03/2025
If you are at @pasteur.fr today, come see @bussigio.bsky.social at 11AM in Salle Retrovirus. You won’t regret it #rna #cryoEM #coolscience @ipdbsc.bsky.social
0113
Max Bonomi @bonomimax.bsky.social · 05/03/2025
Looking forward!!!
010
Reposted by Max Bonomi
PLUMED @plumed.org · 04/03/2025
The paper describing our community effort to collect and organize #plumed tutorials has been published in the Journal of Chemical Physics, as part of the Michele Parrinello Festschrift! doi.org/10.1063/5.02...
doi.org
PLUMED Tutorials: A collaborative, community-driven learning ecosystem
In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes
03010
Max Bonomi @bonomimax.bsky.social · 27/02/2025
Always a pleasure Paul!!!
010
Max Bonomi @bonomimax.bsky.social · 16/02/2025
This might be controversial: what can we learn about IDPs from Alphafold? Starting soon in Room 502B #bps2025
0171
Max Bonomi @bonomimax.bsky.social · 15/02/2025
Thanks Nadia! I was fighting the jet-lag 🏋️‍♀️
010
Max Bonomi @bonomimax.bsky.social · 15/02/2025
Biopolymers in vivo symposium #bps2025 starting soon in Room 408A 🎉
1170
Max Bonomi @bonomimax.bsky.social · 10/02/2025
We had another talk scheduled from Samiran Sen, who unfortunately is not able to come as the US Embassy did not provide a visa in time 😔
020
Max Bonomi @bonomimax.bsky.social · 10/02/2025
Last but not least, Vincent Schnapka will answer the question “Can AlphaFold help us refine ensembles of intrinsically disordered proteins?” on Sunday at 9h45 in Room 502B
160
Max Bonomi @bonomimax.bsky.social · 10/02/2025
Carla Cabal-Fernandez will illustrate how to design a universal fab-binding meditope to use antibody fabs as structural chaperones in cryo-EM on Sunday at 17h45 in Room 502A
100
Max Bonomi @bonomimax.bsky.social · 10/02/2025
Samuel Hoff will show how to expand the chemical space of ligands for virtual screening using cryo-EM structural ensembles on Wednesday at 9h30 in Room 515A
100
Max Bonomi @bonomimax.bsky.social · 10/02/2025
Max will talk about “Integrative Structural Biology in the era of AI” on Saturday at 10h45 in Room 408A
110
Max Bonomi @bonomimax.bsky.social · 10/02/2025
Come meet our lab at #bps2025 in Los Angeles, starting this Saturday. We have 4 talks and 3 posters this year 🎉 More info 👇 @institutpasteur.bsky.social @cnrsbiologie.bsky.social
1212
Max Bonomi @bonomimax.bsky.social · 16/01/2025
Welcome 🎉🎉🎉
0100
Max Bonomi @bonomimax.bsky.social · 23/12/2024
He is not going far 😛
030
Max Bonomi @bonomimax.bsky.social · 10/12/2024
Welcome @plumed.org 🎉
0170
Reposted by Max Bonomi
Bussi Lab @bussilab.org · 06/12/2024
📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at www.plumed-tutorials.org
arxiv.org
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, ef...
26024
Max Bonomi @bonomimax.bsky.social · 06/12/2024
Do you want to work at the interface of molecular simulations, structural biology experiments and #AI? Come to Paris for a PhD at @pasteur.fr 1 PhD position is available in our lab funded by ERC_Research. Please repost!! #compchem #compbio Info 👇 research.pasteur.fr/b/15Hr
research.pasteur.fr
One PhD thesis in integrative structural biology | Research - Institut Pasteur
15340