Arriën Symon Rauh
@asrauh.bsky.social
Postdoc @Fraser lab UCSF Learning dynamics from structural data 🇺🇸 Formerly: computationally studying IDPs in the KLL lab 🇩🇰
AF-CALVADOS is now published doi.org/10.1002/pro.... We combine AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale: — Ensembles of >12000 full-length human proteins — Comparison of IDRs alone and I n context for >1500 TFs @sobuelow.bsky.social @kejohansson.bsky.social
*Preprint Alert*: How do we measure resolution when biomolecules won't sit still? 🔬 Estimating it for a static cryo-EM reconstruction is standard. But what about a conformational ensemble? arxiv.org/abs/2606.14449 with the amazing henryhmattingly.bsky.social and @lukeevanshandle.bsky.social #cryoEM
Excited to share our work describing structural ensembles of protein folding intermediates on the ribosome is now published in @natsmb.nature.com ! www.nature.com/articles/s41... Very grateful to co-first author @sammyhschan.bsky.social, our supervisor John Christodoulou and all our co-authors.
Structures of protein folding intermediates on the ribosome - Nature Structural & Molecular Biology
Atomistic structural ensembles of protein folding intermediates on the ribosome are resolved by comprehensive 19F nuclear magnetic resonance analyses integrated with molecular dynamics simulations, pr...
nature.com
Excited to announce this postdoc position at the intersection of experiment and computation for time-resolved cryo-EM! It's a collaboration between the Enchev group at the Crick and myself and @pilarcossio.bsky.social at the Flatiron Institute! Plz share. crick.wd3.myworkdayjobs.com/External/job...
Senior Data Scientist
Salary for this Role: From £53,025 per annum plus benefits, subject to skills and experience Job Title: Senior Data Scientist Reports to: Radoslav Enchev Closing Date: 06/May/2026 23.59 GMT Job Descri...
crick.wd3.myworkdayjobs.com
Year 3 of Conformational Ensembles Conference! The most compelling questions in structural biology cannot be effectively addressed with a single structure. We have a stellar lineup of people looking at and answering these questions. @fraserlab.com More information: conformationalensembles.github.io
Conformational Ensemble
conformationalensembles.github.io
After three inspiring days filled with excellent science our @cecamevents.bsky.social meeting has come to an end!
New preprint on how disagreement among variant effect predictors can help guide prioritization of proteins for experimental analysis Work led by Nicolas F Jonsson in a collaboration with Joe Marsh. Preprint: doi.org/10.64898/202... @vxh357.bsky.social @jmarshlab.bsky.social 1/6
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 5mo agoDisagreement among variant effect predictors guides experimental prioritization of target proteins https://www.biorxiv.org/content/10.64898/2026.03.18.712765v1
Radial is live! A new organization at @asterainstitute.bsky.social bringing together structural biologists, engineers, and ML scientists to redesign how we do science. @statnews.com has the story: www.statnews.com/2026/03/11/r...
New nonprofit launches with at least $500 million to modernize scientific process for AI era
A new nonprofit called Radial is launching with at least $500 million to modernize the scientific process for the AI era.
statnews.com
How do DNA sequence and histone composition modulate nucleosome plasticity? We investigated this by comparing the behaviour of 40 chemically different nucleosomes. Check our preprint below.
Julia Maristany@juliamaristany.bsky.social · 6mo agoNew paper alert from the group!! 🚨: DNA flexibility tips the balance between stability and plasticity in nucleosomes One of the works from my PhD, co-led alongside @nachper.bsky.social, is finally out! Work from @rcollepardo.bsky.social & @janhuemar.bsky.social ⬇️ www.biorxiv.org/content/10.6... ⬆️
Really excited to share the latest work from my PhD with @giuliotesei.bsky.social and @lindorfflarsen.bsky.social!
Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · 6mo agoNew preprint with work led by @asrauh.bsky.social in which we explore how double mutant cycles could be used to study molecular interactions in condensates, and highlight difficulties in extracting information about interactions from mutational experiments www.biorxiv.org/content/10.6...
Want to learn about how we use computational approaches at different scales to study biomolecular condensates? Check out our latest review, out in Advances in Physics X @juliamaristany.bsky.social @alinaemelianova.bsky.social @rcollepardo.bsky.social www.tandfonline.com/doi/epdf/10....
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale See preprint for: — Ensembles of >12000 full-length human proteins — Analysis of IDRs in >1500 TFs 📜 doi.org/10.1101/2025... 💾 github.com/KULL-Centre/...
bioRxiv Biophysics@biorxiv-biophys.bsky.social · 10mo agoAF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level https://www.biorxiv.org/content/10.1101/2025.10.19.683306v1
Excited to see our review now on arXiv, written together with @fpesce.bsky.social and @lindorfflarsen.bsky.social doi.org/10.48550/arX...
Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · 11mo agoNew review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴 doi.org/10.48550/arX...
New preprint is out ! Bad news : current all-atom simulations of phosphorylated IDPs are very probably wrong (and yes, this is clickbaity on purpose 😇) Good news : we know what to blame for it, and we even have an idea of how to fix it !
bioRxiv Biochemistry@biorxiv-biochem.bsky.social · 11mo agoSticky salts: overbinding of monovalent cations to phosphorylations in all-atom forcefields https://www.biorxiv.org/content/10.1101/2025.08.28.672842v1
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
authors.elsevier.com
Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.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...
Arriën & Giulio's paper on A coarse-grained model for disordered proteins under crowded conditions (that is the CALVADOS PEG model) is now published in final form: dx.doi.org/10.1002/pro.... @asrauh.bsky.social @giuliotesei.bsky.social
Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.CALVADOS 🤝 PEG Work from @asrauh.bsky.social on a simple model for polyethylene glycol to study the effects of crowding on IDPs
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...
bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.AF2χ: Predicting protein side-chain rotamer distributions with AlphaFold2 https://www.biorxiv.org/content/10.1101/2025.04.16.649219v1
Led by @sobuelow.bsky.social & @giuliotesei.bsky.social we put together a full overview of the CALVADOS software and applications. Give it a read: doi.org/10.48550/arX... Give it a try: github.com/KULL-Centre/...
Software package for simulations using the coarse-grained CALVADOS model
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS...
doi.org
Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.Do you like CALVADOS but are not quite sure how to make it? We’ve got your back! @sobuelow.bsky.social & @giuliotesei.bsky.social—together with the rest of the team—describe our software for simulations using the CALVADOS models incl. recipes for several applications. 1/5 doi.org/10.48550/arX...
Thanks to @lindorfflarsen.bsky.social and all authors for this wonderful project on predicting IDR phase separation from sequence! Check out the published version (including added exp. data from @tanjamittag.bsky.social) and feel free to try out our webserver.
Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.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
Very happy to share our next extension to the CALVADOS protein force field: If you want to explore the changes in global dimensions of a disordered protein upon phosphorylation: give it a read and a try! Big thank you to @giuliotesei.bsky.social, @lindorfflarsen.bsky.social and Gustav S. Hedemark
Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.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...
Excited to share our PEG model for disordered proteins in CALVADOS! If you are interested in exploring the effects of a crowder on the global dimensions of an IDP or want to explore the phase separation behaviour of a more weakly PS-prone IDP, have a look at our preprint and give it a try.
Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.CALVADOS 🤝 PEG Work from @asrauh.bsky.social on a simple model for polyethylene glycol to study the effects of crowding on IDPs
www.biorxiv.org/content/10.1...
Molecular grammars of intrinsically disordered regions that span the human proteome
Intrinsically disordered regions (IDRs) of proteins are defined by functionally relevant molecular grammars. This refers to IDR-specific non-random amino acid compositions and non-random patterning of...
biorxiv.org
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...
Check out @rasmusnorrild.bsky.social's work with Alex Buell and Joe Rogers developing and using Condensate Partitioning by mRNA-Display to probe phase separation of ~100.000 sequences, and @sobuelow.bsky.social's simulations to support and analyse the experiments www.biorxiv.org/content/10.1...
Rasmus Krogh Norrild@rasmusnorrild.bsky.social · 2y agoWe are finally ready to share the preprint version about our use of mRNA-display to study what makes disordered proteins form condensates, at the proteome-scale! Check it out here:
In our new paper we characterize the effects of indel variants on protein folding and stability using a new yeast-based protein folding sensor. The work was led by Sven Larsen-Ledet and supported by the @novo-nordisk.bsky.social. Link to paper: www.cell.com/structure/fu...
Systematic characterization of indel variants using a yeast-based protein folding sensor
Larsen-Ledet et al. developed a yeast-based protein folding sensor to determine the effects of indel variants in DHFR. Using a saturated indel library, it was found that most indels are not tolerated. Several are temperature sensitive and folding is rescued by methotrexate. Rosetta and AlphaFold2 predictions correlate with the observed effects.
cell.com
Meet the CALVADOS RNA model Ikki Yasuda, Sören von Bülow & Giulio Tesei have parameterized a simple model for disordered RNA. Despite it's simplicity (no sequence, no base pairing) we find that it captures several phenomena that depend on the charge, stickiness and polymer properties of RNA 🧬🧶🧪
bioRxiv Biophysics@biorxiv-biophys.bsky.social · 2y agoA coarse-grained model of disordered RNA for simulations of biomolecular condensates https://www.biorxiv.org/content/10.1101/2024.11.26.625489v1
If you are a PhD student and like protein disorder (or want to learn more), Birthe Kragelund @bbkrage.bsky.social and Kristian Strømgaard are organizing a PhD course on How IDPs work 🧶🧬🧪 Note the cost if you are not at a Danish university. Details: phdcourses.ku.dk/DetailKursus...
New collaborative work in collaboration with the labs of Robert Best & Tanja Mittag driven by Ben Schuler. Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations. pubs.acs.org/doi/10.1021/...
Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations
It has become increasingly evident that the conformational distributions of intrinsically disordered proteins or regions are strongly dependent on their amino acid compositions and sequence. To facili...
pubs.acs.org
