Gräter lab

Flabby, flexible, and full of potential: Researchers at HITS and @mpip-mainz.mpg.de have developed a #machinelearning model that designs flexible proteins – even with rare patterns. A leap toward next-gen enzymes, therapeutics & sustainable biotech! 🌱💊🔬

👉 Read more: www.h-its.org/2025/07/23/f...

Want your de novo designed protein to be wobbly? 🍮 Seva, Leif & team have made it possible - you find them at ICML! 🤩 @mpip-mainz.mpg.de @hitsters.bsky.social

You want to make your simulations reactive, at little cost? Try KIMMDY. Don't hesitate to reach out if you want to include your favorite chemistry. Super happy to see this online, kudos to the team!

www.biorxiv.org/content/10.1...

Grappa – a machine learned molecular mechanics force field Simulating large molecular systems over long timescales requires force fields that are both accurate and efficient. In recent years, E(3) equivariant neural networks have lifted the tension between computational efficiency and accuracy of force fields, but they are still several orders of magnitude more expe

I thought GRAPPA would also make a nice name (going with the MARTINI, CALVADOS etc... trend) and it turns out it already exists ! It's a model from the @graeterlab.bsky.social :
pubs.rsc.org/en/content/a...

Congrats, Arne!

Join us at the MPIP in Mainz - a few days left to apply! You feel this matches your research agenda but would be a step too early in your career? Do apply!

@rebecca-wade.bsky.social @graeterlab.bsky.social @janstuehmer.bsky.social @astroinformatics.bsky.social @leif-seute.bsky.social

Fantastic news, congratulations, Pascal!

Registration Deadline Extended!
The SIMPLAIX Workshop 2025 is just around the corner, and there's still time to join us!

📅 New deadline: 13 April 2025
📍 Studio Villa Bosch, Heidelberg
🔗 Register now: simplaix-workshop2025.h-its.org

Spots are filling fast — secure yours today! #SIMPLAIX25

Kai's work among 'Most popular articles 2024' in Chem Sci - many thanks to the readers :-)
tinyurl.com/4yb78j5e

Link to our work to predict energy barriers from reactants without DFT: tinyurl.com/5cm4h3ka

@hitsters.bsky.social @mpip-mainz.mpg.de

Max Planck Research Group Leader (W2) in Molecular Design We are looking for exceptional early-career scientists conducting computational research with a proven record of accomplishment. The primary focus of this call is on candidates proposing research on b...

Job alert: Join us in Mainz as

Max Planck Research Group Leader (W2) in Molecular Design

...and make your own research dreams happen on de novo design, generative models, proteins, materials ...
tinyurl.com/r2xjxnuk

@mpip-mainz.mpg.de

A while online now already: Predict the barrier of a reaction without knowing the transition state and in the low data regime using Gaussian Process regr.

Led by Evgeni Ulanov, with Ghulam, Kai and Pascal Friederich @ KIT.
@mpip-mainz.mpg.de @hitsters.bsky.social

pubs.rsc.org/en/content/a...

NeurIPS participation in Europe We seek to understand if there is interest in being able to attend NeurIPS in Europe, i.e. without travelling to San Diego, US. In the following, assume that it is possible to present accepted papers ...

Would you present your next NeurIPS paper in Europe instead of traveling to San Diego (US) if this was an option? Søren Hauberg (DTU) and I would love to hear the answer through this poll: (1/6)

Wondering how to predict protein flexibility in a sec? No time to run MD simulations but want to go beyond pLDDT? Check out BBFlow
arxiv.org/html/2503.05...

Useful in particular for de novo designs.

Led by Nico Wolf & Leif Seute, w Seva, Simon, and Jan. @mpip-mainz.mpg.de @hitsters.bsky.social

Crash testing machine learning force fields for molecules, materials, and interfaces: model analysis in the TEA Challenge 2023 Atomistic simulations are routinely employed in academia and industry to study the behavior of molecules, materials, and their interfaces. Central to these simulations are force fields (FFs), whose de...

#compchem Good read: Crash testing machine learning force fields for molecules, materials, and interfaces: model analysis in the TEA Challenge 2023 #compchemsky doi.org/10.1039/D4SC...

YouTube video by TheHITSters HITS-SIMPLAIX Joint Colloquium: Cecilia Clementi on protein dynamics and Machine Learning

Curious about how Machine Learning and Molecular Simulations are used to model Protein Dynamics?

Then watch our HITS-SIMPLAIX Joint Colloquium with Cecilia Clementi @cecclementi.bsky.social which is now available on our YouTube channel.

www.youtube.com/watch?v=2HAI...

#aufstehenfuerdemokratie

Don't miss our next HITS-SIMPLAIX Joint Colloquium on 10 February at 2:00 PM CET! Cecilia Clementi @cecclementi.bsky.social will talk about Modeling Protein Dynamics with Machine Learning and Molecular Simulation. Sign up ow.ly/h0Wl50UQ2kX to join via Zoom or just come by. @simplaix.bsky.social

Thanks! If you talk metal ions you will need to train it for such systems, we haven't. Others got in touch with us that use it for this purpose - happily so far I think ;-)

This was a very interesting paper to help supervise because it’s a totally different way to think about DNA structure, and uses a sequencer in a very creative way to understand DNA breakage. Check it out! 🧬

Need forcefield parameters for a weird small molecule, modified nucleotide, or non-natural amino acid? Check out Grappa, a GNN approach to generating bonded parameters compatible with the MD engine of your choice! 🧬

Grappa – a machine learned molecular mechanics force field Simulating large molecular systems over long timescales requires force fields that are both accurate and efficient. In recent years, E(3) equivariant neural networks have lifted the tension between co...

Grappa is out: pubs.rsc.org/en/content/a...

We are looking forward to feedback from and extensions by the community! Try it out for your favorite (bio)molecules - ligands, post-translational modifications, metal-enzymes, DNA, ...

Gräter lab (@graeterlab.bsky.social) We aim at unraveling the intricacies of molecular perception and designing sensing molecular systems from the ground up. We work at the interface of biophysics, biochemistry, and materials science. @ Max Planck Institute for Polymer Research, Mainz.

You find us here:
https://bsky.app/profile/graeterlab.bsky.social

A long journey has taken the next step. Yesterday we defended our Cluster of Excellence Proposal #CoM2Life Communicating Biomaterials at the DFG. What an amazing journey with an amazing team. #teamscienceisthedreamscience @unimainz.bsky.social @tuda.bsky.social @mpip-mainz.mpg.de

Sequence-specific, mechanophore-free mechanochemistry of DNA Nucleic acids, such as DNA, are integral components of biological systems in that they steer many cellular processes and biotechnological applications…

Where does DNA break when pulled? We can tune it! Paper led by Johannes Hahmann, MD simulations by Boris, great collaboration with Herrmann and Goestl labs @ RTWH

www.sciencedirect.com/science/arti...

🥲... and very excited to start from January with full forces at the MPIP@Mainz, with many (most) of my awesome lab members - and some HITS spirits - tagging along

Stereochemistry in the disorder–order continuum of protein interactions Nature - Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.

Have you looked in the mirror recently? We took a good look at stereochemistry and how D- and L-ligands bind ... its all about disorder! Exited to share a true REPIN collaborative work led by @estellaan.bsky.social, A. Due and J. Olsen. Thanks for support NNF and DFF.
rdcu.be/d1F6q

🚨 Preprint Alert! 🚨
Check out our new book chapter on Constant-pH MD Simulations of Lipids! Learn how to use CpHMD simulations to study pH-dependent behavior of aminolipids in lipid nanoparticles for drug delivery. 💊🧬
#membranes #LNP @m-a-r-i-u-s.bsky.social @fau.de
biorxiv.org/cgi/content/...

Protein design is one of my new favorites :-) thanks to our best friends, #proteins, and to the fun team behind this👇 https://x.com/JanStuehmer/status/1865403885759705428

Mark your calendars for the HITS-SIMPLAIX Joint Colloquium on “Computational Protein Dynamics in the Era of Machine-Learned Atomistic Simulations” on 16 December, 2pm CET. Email events@h-its.org for on-site participation or register here ow.ly/UoUL50UlAa5 to join via Zoom.