Congratulations, Matthieu! 🥳

Very happy to release AutoMartiniM3 for Martini3 to automatize CG modelling of small molecules and fragments.

Great work from M Szczuka in my lab in collab with @pauloctsouza.bsky.social and @tbereau.bsky.social teams!

Give it a try: github.com/Martini-Forc...

poke @cg-martini.bsky.social

Associate Principal Scientist: Molecular Modeling, Analytical Research & Development job in Rahway, New Jersey, United States of America | jobs at Merck migration Apply for Associate Principal Scientist: Molecular Modeling, Analytical Research & Development job with Merck migration in Rahway, New Jersey, United States of America. Browse and apply for the jobs a...

Very excited to be recruiting for an Associate Principal Scientist: Molecular Modeling, Analytical Research & Develop. Our Digital Sciences team is seeing many requests related to influencing formulation design, especially for biologics. #chemjobs #compchem #chemsky jobs.merck.com/us/en/job/R3...

Martini workshop registration now open !!!!
See cgmartini.nl for details and how to apply.
Looking forward to seeing you in Groningen, Aug 11-15th.

Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates - Nature Communications Here, the authors implement molecular dynamics simulations to model ATP-driven enzymatic reactions, revealing how the enzyme CK1δ phosphorylates condensates of the neurodegeneration linked protein TDP...

🚨Publication alert🚨
"Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates" by Emanuele Zippo, @lstelzl.bsky.social, @dormannlab.bsky.social & Thomas Speck. Congratulations!!
📄 www.nature.com/articles/s41...
#TDP43 #CK1δ #ALS #biophysics #proteincondensates

Pre-announcement: MARTINI tutorial workshop, August 11-15th 2025 in Groningen, The Netherlands !!
Learn basic and advanced Martini from the cocktail masters themselves. Registration will open soon.

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social

🔗 Preprint here tinyurl.com/3a74uanv

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

Our paper on prediction of phase-separation propensities of disordered proteins from sequence is now published:
www.pnas.org/doi/10.1073/...

The paper has been substantially updated compared to the preprint including new experimental data and using the neural network to finetune CALVADOS. 1/n

We’re looking for fellow nerds to help us make disordered proteins druggable. Love #IDPs, #MD, #NMR, #AI, #DrugDiscovery, or #MassSpec? Let’s talk.
@bindresearch.org is hiring across the board: bindresearch.org/careers/
#compchem #compbio #NMRChat #TeamMassSpec #chemjobs @chemjobber.bsky.social

Martini3-IDP: improved Martini 3 force field for disordered proteins - Nature Communications Here, the authors introduce Martini3-IDP, a refined model for disordered proteins that addresses prior over-compact structures. Validated across diverse systems, it captures IDP interactions and biomo...

Martini 3 - IDP is out! Improved parameters for disordered proteins, great work from Liguo Wang: www.nature.com/articles/s41...

We are organizing a conference for young researchers at the intersection between physics & biology: www.embl.org/about/info/c... @embl.org @events.embl.org @intcha.bsky.social
Please consider applying/registering -- the deadline is already in one week!

Airplane

Traveling to San Diego for ACS. Really looking forward to the meeting ☺️.l!

CALVADOS now has parameters for phosphorylated amino acids

@asrauh.bsky.social @giuliotesei.bsky.social and Gustav Hedemark used a top-down approach in which we targeted experimental data to derive parameters or phosphorylated serine and threonine doi.org/10.1101/2025...

Protein dynamics was the first research to enchant me >10yrs ago, but I left in PhD bc I couldn't find big experimental data to evaluate models.

Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1.
📝: rb.gy/de5axp

Expanded ensemble predictions of toluene–water partition coefficients in the SAMPL9 log P challenge The logarithm of the partition coefficient (log P) between water and a nonpolar solvent is useful for characterizing a small molecule's hydrophobicity. For example, the water–octanol log P is often us...

New paper from the Voelz Lab in @pccp.rsc.org! Goold et al. performed many parallel expanded ensemble free energy simulations on @foldingathome.org using GROMACS (@gromacs.bsky.social) with OpenFF 2.0 (@openforcefield.org) to make blind logP predictions in SAMPL9

doi.org/10.1039/D4CP...

Seed structure and phosphorylation in the fuzzy coat impact tau seeding competency Tau is a pathogenic protein in Alzheimer's (AD) and other neurodegenerative diseases. The misfolding of tau into beta-sheet rich elongated filaments is thought to be a key event in disease pathogenesi...

Cool stuff from our collaboration with @mxhend.bsky.social: the fold of tau filaments matters for seeding in primary cultures & in live mice: the AD fold is more seeding efficient than non-AD folds! But that's not all: phosphorylation of the fuzzy coat matters too. 🤩

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

Multi-scale classification decodes the complexity of the human E3 ligome E3 ubiquitin ligases are key regulators of protein homeostasis, targeting specific proteins for degradation via the ubiquitin-proteasome system (UPS). They provide crucial substrate specificity, makin...

Just dropped on bioRxiv! Our team has assembled a data-driven map of the human E3 ligome. Check out our preprint! #E3_ligome #ubiquitination #dataIntegration #metriclearning www.biorxiv.org/content/10.1...

Figure from the paper illustrating sequence–ensemble–function relationships for disordered proteins. ML prediction (black) and design (orange) approaches are highlighted on the connecting arrows. Prediction of properties/functions from sequence (or vice versa, design) can include biophysics approaches via structural ensembles, or bioinformatics approaches via other hetero- geneous sources. The lower panels show examples of properties and functions of IDRs for predictions or design targets. ML, machine learning; IDRs, intrinsically disordered proteins and regions.

Our review on machine learning methods to study sequence–ensemble–function relationships in disordered proteins is now out in COSB

authors.elsevier.com/sd/article/S...
Led by @sobuelow.bsky.social and Giulio Tesei

Go and work with @reidalderson.bsky.social !!!

New Preprint ‼️ Work led by the incredible @ananyac2000.bsky.social 💃🏽💃🏽 Mpipi-T is finally here!!! 🥳🥳 👇🏽👇🏽

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

Prediction of small-molecule partitioning into biomolecular condensates from simulation Predicting small-molecule partitioning into biomolecular condensates is key to developing drugs that selectively target aberrant condensates. However, the molecular mechanisms underlying small-molecul...

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

CALVADOS 🤝 PEG

Work from @asrauh.bsky.social on a simple model for polyethylene glycol to study the effects of crowding on IDPs

We’re hiring a computational biologist in Heidelberg DE or Stevenage UK to work on a pretty ambitious project with fun people for the year www.linkedin.com/jobs/view/41...

Table of Contents figure showing the CALVADOS-RNA model and a snapshot from a mixed protein-RNA condensate

CALVADOS-RNA is now published
doi.org/10.1021/acs....

This is a simple model for flexible RNA that complements and works with the CALVADOS protein model. Work led by Ikki Yasuda who visited us from Keio University.

Try it yourself using our latest code for CALVADOS
github.com/KULL-Centre/...

Remembering Professor Béla Novák 1956 - 2025 With great sadness, we announce the loss of Professor Béla Novák.

A brilliant, kind, funny colleague gone too soon. We will miss you Bela.
www.merton.ox.ac.uk/news/remembe...

Congratulations!!!

DPhil in Biomedical and Clinical Sciences (Oxford-GSK) | University About the courseThe DPhil in Biomedical and Clinical Sciences (Oxford-GSK) aims to address an unmet need among clinicians for training in data science and translational medicine. The course provides

Great opportunity for clinicians to gain early-career experience in a fully-funded, translational medicine programme in Oxford.
If you know anyone interested, please share this link. There is a wide range of projects, including mine. Deadline Fr 14 March 2025
www.ox.ac.uk/admissions/g...

The BioEmu-1 model and inference code are now public under MIT license!!!

Please go ahead, play with it and let us know if there are issues.

github.com/microsoft/bi...

Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates Biomolecular condensates composed of highly charged biomolecules, such as DNA, RNA, chromatin, and nucleic-acid binding proteins, are ubiquitous in the cell nucleus. The biophysical properties of thes...

Introducing Mpipi-Recharged🔥🔥🔥

Our Mpipi coarse-grained model for biomolecular condensates now includes a pair-specific electrostatic potential that improves its predictions, including for challenging charged systems—all while still treating solvent and ions implicitly

pubs.acs.org/doi/10.1021/...