We (@sobuelow.bsky.social & @kejohansson.bsky.social) tested AF-CALVADOS using the recently described PeptoneBench SAXS benchmark that contains SAXS data for >400 proteins with different amounts of order and disorder. The results look pretty good 😇 so we are sharing here while updating the preprint📝

Our review on Integrative modelling of biomolecular dynamics 💃 is now live at COSB We discuss approaches to integrate computational methods with time-dependent & time-resolved experiments to study protein dynamics With @dariagusew.bsky.social & Carl G. Henning Hansen doi.org/10.1016/j.sb...

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

Our story on GroEL/ES action during cotranslational folding is now published @natcomms.nature.com. Led by former-student Alzbeta Roeselova, and in collaboration with Rado Enchev's lab @crick.ac.uk. www.nature.com/articles/s41...

My first full contribution from my time in @opig.stats.ox.ac.uk is now out! Together with @fspoendlin.bsky.social (and with contributions from King Ifashe), we created FlAbDab and FTCRDab: two large-scale, open molecular dynamics datasets to study flexibility in immune receptors.

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

I'm hiring for a PhD position at Malmö University, Sweden! The project will focus on molecular modelling of proteins, lipids, and biomolecular condensates at cell membranes. More details and application form: tinyurl.com/4zm92365 Please feel free to share! @vetenskapsradet.bsky.social | @mau.se

So excited that our lab's first home-grown paper is now available on ChemRxiv! Kinetic NMR screening: rapidly quantifying fast ligand dissociation in fragment mixtures using ¹⁹F relaxation dispersion | doi.org/10.26434/che... 🧲🧪

Excited to see our review now on arXiv, written together with @fpesce.bsky.social and @lindorfflarsen.bsky.social doi.org/10.48550/arX...

Our paper on: A coarse-grained model for simulations of phosphorylated disordered proteins (aka parameters for phospho-serine and -threonine for CALVADOS) is now published in Biophysical Journal authors.elsevier.com/a/1lTcE1SPTB... @asrauh.bsky.social @giuliotesei.bsky.social & Gustav Hedemark

New preprint with Benjamin Lang, Richard Kriwacki, John Christodoulou, and M. Madan Babu! www.biorxiv.org/content/10.1... Protein Dynamics at Different Timescales Unlock Access to Hidden Post-Translational Modification Sites #bioinformatics #compchem #folding #proteindynamics

Now published in Advanced Science: our latest study combining NMR and MD to investigate a transient folding intermediate of human lysozyme #nmrchat #compchem

In press!! NMR & MD simulations reveal how non-native contacts stabilise a key transient intermediate in the lysozyme amyloid cascade. Well done Minkoo and all!! @phar.cam.ac.uk For CMD ❤️ advanced.onlinelibrary.wiley.com/doi/10.1002/...

The third episode of The Tortured Proteins Department is out now! We chatted about grant cancellations, exciting regional meetings and reunions, two fun new preprints, community norms around code release, and the importance of giving kudos. @fraserlab.com

Led by @vvouts.bsky.social in @rhp-lab.bsky.social, we measured the degron potency of >200,000 30-residue tiles from >5,000 cytosolic human proteins and trained an ML model for degrons 📜 www.biorxiv.org/content/10.1... 🖥️ github.com/KULL-Centre/...

Rationally designing 19F probe pairs was key to determining the structures of protein folding intermediates on the ribosome in our latest preprint. Our design strategy is now published in @natcomms.nature.com www.nature.com/articles/s41... #NMRchat #compbio #compchem

Our latest is now in Nature Communications: www.nature.com/articles/s41... Rational design of fluorine NMR labelling sites (AlphaFold/molecular dynamics) to gain insights into protein structure and interactions for large complexes and in cells! #NMRchat #compchem #AlphaFold #proteinfolding

Presenting one of my favorite manuscripts I've ever worked on: "Characterizing structural and kinetic ensembles of intrinsically disordered proteins using writhe" www.biorxiv.org/content/10.1... by Tommy Sisk, with a generative modeling component done in collaboration with @smnlssn.bsky.social

AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...

Excited to share our new preprint presenting mechanistic details of how proteins fold on the ribosome. With co-first author @sammyhschan.bsky.social , @twlodarski.bsky.social , Alkistis Mitropoulou, Lisa Cabrita, and John Christodoulou. www.biorxiv.org/content/10.1... #proteinfolding #compchem #NMR

Structures of protein folding intermediates on the ribosome https://www.biorxiv.org/content/10.1101/2025.04.07.647236v1

Cryo-EM, and integration with MD simulations, of nascent proteins on the ribosome. Congrats Alki and @twlodarski.bsky.social and co-authors!

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

Gemma Solomon and I are looking for a postdoc to work across the two groups on modelling biological systems with a view to applications for quantum computing More details about the project including how to apply in the link below. Deadline April 9 2025 candidate.hr-manager.net/ApplicationI...

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...

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.

Preprint! The ribosome’s electro charge defines how proteins fold by all-atom MD and 19F NMR. Led by @julianstreit.bsky.social with @charles-burridge.bsky.social, Joel Wallace, @chriswaudby.bsky.social, Lisa Cabrita, John Christodoulou #nmrchat #compchem #compbio doi.org/10.1101/2025.02.10.637539

Check out our latest preprint on the role of the ribosome in the folding of its nascent polypeptides - an integrative study combining NMR experiments and atomistic simulations! #NMRchat #compchem #CompBio #ribosome #proteinfolding www.biorxiv.org/content/10.1...

How do proteins mis-fold? Paper led by Jacob Aunstrup from Alex Büll’s lab with MD simulations by Abigail Barclay, and key contributions from several others. We combined measurements of Φ-values with MD simulations to study the transition state for amyloid fibril growth doi.org/10.1038/s415...

Are PDB models biased in terms of how well they explain the underlying experimental data and are modeled? www.biorxiv.org/content/10.1...

Out now! How to rationally design 19F labels to study structures of large biomol complexes, incl in cells. Using engineered ring currents, and designed with MD and AF. With co-first author Julian Streit, and Saifu Daya and John Christodoulou. #nmrchat #compchem www.biorxiv.org/content/10.1...