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Reposted by Giulio Tesei

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 08/09/2026

In 2017 I co-organized a BPS thematic meeting on Conformational Ensembles from Experimental Data and Computer Simulations We're back in Berlin Aug 2027 with Biomolecular Dynamics: Integrating Experiments and Computation with a great line-up (to be revealed soon) www.biophysics.org/upcoming-the...

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Reposted by Giulio Tesei

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/08/2026

Two new CALVADOS preprints Coarse-grained models for simulations of double-stranded nucleic acids for mixed protein-nucleic acid condensates doi.org/10.64898/202... MEM-CALVADOS: A Residue-Level Model for Flexible Proteins at Membrane Interfaces doi.org/10.64898/202...

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Giulio Tesei @giuliotesei.bsky.social · 18/08/2026

Happy to share our new preprint on MEM-CALVADOS! Work led by @rsaltutti.bsky.social extending CALVADOS to flexible proteins at lipid membrane interfaces. 🗞️ doi.org/10.64898/202... 🖥️ github.com/gitesei/MEM-... @vetenskapsradet.bsky.social

Schematic showing the combination of CALVADOS with a coarse-grained lipid model, resulting in MEM-CALVADOS, illustrated using T-cell signaling proteins LAT (cyan), Grb2 (blue), and Sos1 PRR (orange).

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 30/05/2026

Everything you wanted to know about the protein chemistry behind how amino-acid changes affect the cellular abundance of proteins from @tkschulze.bsky.social Effects of residue substitutions on the cellular abundance of proteins doi.org/10.7554/eLif...

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 14/04/2026

Run an MD simulation of any protein in the AlphaFold Protein Structure Database using AF-CALVADOS Thanks to @sobuelow.bsky.social AF-CALVADOS is now on Colab colab.research.google.com/github/KULL-...

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Reposted by Giulio Tesei

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 16/03/2026

We are hiring a postdoc in computational biophysics and machine learning studies of intrinsically disordered proteins We aim to study the function of IDPs by combining CG MD, ML and bioinformatics in collaboration with @tanjamittag.bsky.social & @rhp-lab.bsky.social tinyurl.com/REWIRE-PD

Postdoc position:Computational Biophysics of Disordered Proteins, Lindorff-Larsen group, University of Copenhagen, Denmark

https://tinyurl.com/REWIRE-PD
Deadline May 3rd, 2026

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Reposted by Giulio Tesei

xavier salvatella @xsalvatella1.bsky.social · 16/03/2026

Our work on how oligomerization can enable selectively targeting intrinsic disorder with small molecules is now out in Science Advances: www.science.org/doi/10.1126/...). Congratulations Stase Bielskute and @borjaml.bsky.social and thanks to the collaborators and funders !

science.org

Oligomerization enables the selective targeting of an intrinsically disordered region by a small molecule

The druggability of intrinsically disordered regions.

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Reposted by Giulio Tesei

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 09/03/2026

Community perspective: Toward a unified framework for determining conformational ensembles of disordered proteins 🍝 with framework for experimental data acquisition, computational ensemble generation & validation Led by @hamidrgh.bsky.social, Silvio Tosatto & Alex Monzon doi.org/10.1038/s415...

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Reposted by Giulio Tesei

Arriën Symon Rauh @asrauh.bsky.social · 09/02/2026

Really excited to share the latest work from my PhD with @giuliotesei.bsky.social and @lindorfflarsen.bsky.social!

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Reposted by Giulio Tesei

Julian Streit @julianstreit.bsky.social · 21/01/2026

New preprint with @invemichele.bsky.social, Sandro Bottaro, Kamil Tamiola, and @lindorfflarsen.bsky.social on transiently structured states of IDPs sampled in atomistic simulations with enhanced sampling and integrated with experimental data.

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Reposted by Giulio Tesei

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 24/01/2026

Integrative structural biology by the sea The Jan 31st deadline for our FEBS advanced course on integrative structural biology is getting closer, so get your applications in for Lost In Integrative Vol. 2 probingbiomolecules2026.febsevents.org network.febs.org/posts/integr...

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Reposted by Giulio Tesei

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 23/01/2026

Looking for something to read over the weekend? Our review on computational design of intrinsically disordered proteins is now published in final form 🍝 With @giuliotesei.bsky.social & @fpesce.bsky.social doi.org/10.1016/j.sb...

Figure illustrating the role of machine learning in IDP design, showing both the training data, machine learning and applications

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Reposted by Giulio Tesei

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 16/01/2026

First preprint of the year, led by Junjie Zhu from Haifeng Chen’s lab Extending Conformational Ensemble Prediction to Multidomain Proteins and Protein Complex doi.org/10.64898/202...

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Reposted by Giulio Tesei

Davide Mercadante @mercadantelab.bsky.social · 07/01/2026

New preprint!🚨 We're finally able to sample secondary structure in coarse-grained simulations of IDPs! 🍝🍝🍝 With an AI-based prediction of NMR chemical shifts in CG simulations, we correct dynamics on the fly, making secondary structure emerge as dictated by expts😍! www.biorxiv.org/content/10.6... 🧵👇

biorxiv.org

Capturing secondary structure in coarse grained intrinsically disordered proteins with simulations driven by chemical shifts.

A major challenge when investigating intrinsically disordered proteins (IDPs) pertains to understanding how secondary structure formation across otherwise disordered ensembles, relates to function. Wh...

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Reposted by Giulio Tesei

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 20/10/2025

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/...

Figure showing the AF-CALVADOS restraining and simulation protocol based on AF2 structure, PAE and pLDDT

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Reposted by Giulio Tesei

Anna Duncan @drannaduncan.bsky.social · 15/10/2025

Registration now open for the '3rd Annual Danish Workshop on Advanced Molecular Simulation' Join us in beautiful Aarhus for a 2-day workshop on biomolecular simulations! 9-10 December 2025 Link for registration: aias.au.dk/events/show/...

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David De Sancho @daviddesancho.bsky.social · 03/10/2025

Check out our latest, where we investigate the molecular origin of differences between Lys and Arg and their roles in biomolecular #condensates @dipcehu.bsky.social www.biorxiv.org/content/10.1...

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Reposted by Giulio Tesei

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 02/10/2025

Integrative modelling of biomolecular dynamics Time-dependent and -resolved experiments combined with computation provide a view on molecular dynamics beyond that available from static, ensemble-averaged experiments Review w @dariagusew.bsky.social & Carl G Henning Hansen doi.org/10.48550/arX...

$Figure 1 from the review. Caption: Comparison of a schematic example showing static, time-dependent, and time-resolved experiments illustrated by a protein folding process. (a) A static experiment measuring the observable O$_{\text{exp}}$ is shown, which can be modelled as a distribution of simulated values, O$_{\text{calc}}$, representing a conformational ensemble of folded and unfolded states. (b) Shows a time-dependent experiment, where the equilibrium dynamics of reversible folding gives rise to measured transition times $\tau_1$ and $\tau_2$. These can be modelled as equilibrium dynamics, illustrated by a free energy (FE) surface along a chosen degree of freedom (D.O.F.) (c) A time-resolved experiment probes a non-equilibrium process, where the system begins at $t_{0}$ in the folded state. During the observation time $t$ the protein unfolds until $t_{\text{max}}$. At each time point, a distinct ensemble average, O$_{\text{exp}}$, can be observed, reflecting the proteins changing structure. This evolution can be modelled as distributions of O$_{\text{calc}}$ at each time point. These are shown together with a FE surface.$

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Giulio Tesei @giuliotesei.bsky.social · 02/10/2025

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

Snapshot of a condensate near a lipid membrane with Swedish Research Council and Malmö University logos.

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Reposted by Giulio Tesei

Sarah Shammas @sarahshammas.bsky.social · 01/10/2025

Why are transcription factors disordered? Come join us in Oxford as a postdoc and we'll find out together! Help publish 3 mature projects, AND develop cool new single molecule fluorescence binding assays! biophysics transcription protein:DNA interactions my.corehr.com/pls/uoxrecru...

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Giulio Tesei @giuliotesei.bsky.social · 18/09/2025

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

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 22/07/2025

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

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/07/2025

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

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/04/2025

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...

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Giulio Tesei @giuliotesei.bsky.social · 15/04/2025

Happy to share a walkthrough of the applications of our package for simulations using CALVADOS! Big thanks to @sobuelow.bsky.social, @lindorfflarsen.bsky.social, and the whole team for making this possible. Thrilled to mark this as my first last-author paper!

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 15/04/2025

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...

Figure showing the architecture of the CALVADOS package.

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 25/03/2025

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

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21/03/2025

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...

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Arriën Symon Rauh @asrauh.bsky.social · 09/03/2025

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.

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 12/03/2025

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

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.

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