Our work on computational design of intrinsically disordered proteins is now out in Science Advances We asked whether we could use molecular simulations and ML to design disordered proteins with specified properties of conformational ensembles 🍝 doi.org/10.1126/sciadv…

The avg. salaries for employees at U. of Copenhagen are out, & when normalized to full profs are Full prof. 100% Assoc. prof. 73% Assist. prof. 61% Post doc. 57% PhD stud. 46% This is before a progressive tax, so post-tax differences will be smaller uniavisen.dk/loenninger-paa…

What an amazing day at yesterday UCPH SCIENCE PhD graduation ceremony! 🎓 And I’m also humbled and excited to announce that I’ve been honored with the PhD Award of the year at SCIENCE 2024.

New preprint w @TKSchulze who analysed cellular abundance (VAMP-seq) data for ~32,000 variants of six proteins We find that much of the variation can be explained and predicted by a burial-dependent substitution matrix Lots more goodies in the paper doi.org/10.1101/2024.0…

Our new research article benchmarks #AlphaFold2’s ability to predict #protein conformational ensembles, comparing it to #molecular #dynamics and #NMR. Promising, but some structural complexities remain undetected. Read here: sciencedirect.com/science/articl…

Cats are invariant under SO(3) transformations! 😼

A great collaboration with KerstinDoerner and Maria Hondele! Also many thanks for the help from Kresten Lindorff-Larsen. We used our CALVADOS model to study the effect of tagging on condensation and phase separation—a good starting point for studying specific interactions.

Our paper on the use of dioxane as a reference for NMR diffusion measurements is now out authors.elsevier.com/a/1jxWn1SPT7tPu This paper led by Emil Tranchant revisits pioneering 25 y old work on using dioxane as a reference. We update the reference value and discuss the implications 1/4

Now it is on Protein Science! (onlinelibrary.wiley.com/doi/10.1002/pr……) We also have a colab version of CALVADOS 3 (colab.research.google.com/github/KULL-Ce……). Looking forward to receiving your feedbacks!

And check out the new CALVADOS code base from @SoBuelow (& Giulio Tesei + Fan Cao) that makes it even easier to run simulations of individual IDRs and multi-domain proteins as well as condensates (incl. multi-component systems) using OpenMM github.com/KULL-Centre/CA…

Sören, Giulio & I wrote a short review on the use of machine learning methods to study disordered proteins, with a focus on linking sequences to ensembles (by simulation or generative models; or for design), biophysical properties and biological functions doi.org/10.48550/arXiv…

COCOMO2: A coarse-grained model for interacting folded and disordered proteins biorxiv.org/cgi/content/sh… #biorxiv_biophys

Meet the CALVADOS RNA model on bioRxiv or on 🦋

📣 Save the dates 📅 We are organizing a Benzon Symposium on "Protein structure prediction and design" with what I think is an amazing set of speakers Meeting will take place in Copenhagen 🇩🇰 on Sept. 1–4, 2025, and abstract submission will open in March

Check out Rasmus Krogh Norrild's work with Alex Buell @biophysics_dtu and Joseph Rogers developing and using Condensate Partitioning by mRNA-Display to probe phase separation of ~100.000 sequences, and @SoBuelow simulations to support and analyse the experiments

It was even marked as a "very important paper". Very happy about this development

Happy Chinese new year! 新春快乐！🥳🎉

CALVADOS-RNA

Do you like CALVADOS but are not quite sure how to make it?