KIMMDY lets simulations watch bonds break and form, not just molecular motion. It scales to millions of atoms and traces reaction chains in proteins and DNA, from collagen chemistry to UV-driven DNA damage.Read more: www.mpip-mainz.mpg.de/1175119/PM20... @hitsters.bsky.social @graeterlab.bsky.social

When molecules react

mpip-mainz.mpg.de

The #mattertolife fall days are a wonderful opportunity to connect to this vibrant community. This time at the @mpip-mainz.mpg.de with talks by the local hosts @graeterlab.bsky.social, @landfesterdept.bsky.social and @weilgroup.bsky.social. Thanks @mattertolife.bsky.social for bringing us here 👍😀🙏

Our #mattertolife Fall Days have just started 👏🏻 Thank you @mpip-mainz.mpg.de for hosting us! @graeterlab.bsky.social @landfesterdept.bsky.social @weilgroup.bsky.social

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

Seva Viliuga@proteinator.bsky.social · last yr.

1/6 One of the key features of functional proteins is their inherent structural flexibility. In our recent work at #ICML, we introduce flexibility to protein structure design! More in a thread below. Code / Tutorial: github.com/graeter-grou... Poster: W-109, Thu 17 Jul 11 a.m. PDT — 1:30 p.m. PDT

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...

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...

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

pubs.rsc.org

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!

Gräter lab @graeterlab.bsky.social · last yr.

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

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

@simplaix.bsky.social · last yr.

The 3-day SIMPLAIX Workshop 2025 is now officially OPEN! 🎉 We’re kicking off an inspiring event filled with keynotes, discussions and networking opportunities on multiscale computer simulation and #machinelearning over the next few days. #SIMPLAIX2025 #AI #lifesciences #materialsscience

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

Chemical Science@chemicalscience.rsc.org · last yr.

We are pleased to announce that our 2024 most popular article collections are now online! Check out the links below for the most popular articles from last year in your field: Analytical Chemistry pubs.rsc.org/en/jour... Catalysis pubs.rsc.org/en/jour...

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

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...

tinyurl.com

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...

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)

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 ...

docs.google.com

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

#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...

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...

doi.org

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...

HITS-SIMPLAIX Joint Colloquium: Cecilia Clementi on protein dynamics and Machine Learning

YouTube video by TheHITSters

youtube.com

#aufstehenfuerdemokratie

Winkler Laboratory@winklerlab.bsky.social · last yr.

📢 It is 5 min before 12❗ "Aufstehen für Demokratie" is committed to fact-based political decisions & democratic processes: www.aufstehenfuerdemokratie.de www.openpetition.de/!ychtb 📅 Join us on Feb 12th at 11:55 am at universities and research institutions in Germany. 🔬 Science needs democracy 🤝

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

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! 🧬

Gräter lab @graeterlab.bsky.social · 2y ago

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...

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! 🧬

Gräter lab @graeterlab.bsky.social · 2y ago

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, ...

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, ...

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...

pubs.rsc.org

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

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.

bsky.app

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

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...

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…

sciencedirect.com

🥲... 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

HITS - Heidelberg Institute for Theoretical Studies@hitsters.bsky.social · 2y ago

After 15 years, we say goodbye to group leader Frauke Gräter (@graeterlab.bsky.social) who will assume her new role as director of the Max-Planck-Institute for Polymer Research in Mainz as of January 2025. Read more about her time at HITS here: www.h-its.org/2024/12/19/f...

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

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.

rdcu.be

🚨 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.