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Reposted by Arriën Symon Rauh

Giulio Tesei @giuliotesei.bsky.social · 20d

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 · 21d

New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴

doi.org/10.48550/arX...

Figure 3 from the paper with the caption: "Role of machine learning in de novo design of IDRs. (A) Machine-learning models can be trained on diverse data sources, from molecular dynamics simulations to annotations of cellular localization and protein structures from the Protein Data Bank. (B) Often implemented as neural networks using sequence-encoded features as input, these models can initially be trained on a limited region of sequence space as surrogate models. Through active learning, additional simulations are performed during the design campaign to generate new data, and the surrogate model is retrained on the expanded dataset to progressively improve its accuracy. (C) Machine-learning models have been developed to predict biophysical observables, biological annotations, and protein structures. When combined, machine-learning models can be used to identify a set of sequences that strike a trade-off between multiple design objectives, defining a Pareto front."

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Jules Marien @marienj.bsky.social · Sep 3

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 · Sep 2

Sticky salts: overbinding of monovalent cations to phosphorylations in all-atom forcefields https://www.biorxiv.org/content/10.1101/2025.08.28.672842v1

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Jul 22

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

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Jul 17

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 · Apr 17

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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Arriën Symon Rauh @asrauh.bsky.social · Apr 15

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/...

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Sören von Bülow @sobuelow.bsky.social · Mar 25

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 · Mar 25

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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Arriën Symon Rauh @asrauh.bsky.social · Mar 21

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 · Mar 21

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 · Mar 9

Big thank you to Giulio Tesei and @lindorfflarsen.bsky.social for their guidance.

The preprint can be found here: www.biorxiv.org/content/10.1...

The code and data are available here: github.com/KULL-Centre/...

A coarse-grained model for disordered proteins under crowded conditions

www.biorxiv.org

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Arriën Symon Rauh @asrauh.bsky.social · Mar 9

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 · Mar 6

CALVADOS 🤝 PEG

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

Figure 3 from the paper showing how the phase separation propensity of WT and aromatic variants of the hnRNPA1-LCD responds linearly to PEG concentration. Panel C shows a "slab" simulation of A1-LCD with 0%, 5% and 10% PEG.

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Mar 1

Preprint submitted 🇺🇦

Figure from manuscript showing epresentative snapshots from slab simulations with 100 chains A1 (dark blue) with w/v-percentages of 0%, 5% (100:127) and 10% (100:254) PEG8000 (orange chains, 181 monomers) illustrating how PEG both lowers the 𝐶sat with increasing concentrations and also increases the effective protein concentration in the condensate (𝐶con).

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Rohit V. Pappu @rohitpappu68.bsky.social · Feb 28

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...

www.biorxiv.org

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Jan 16

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...

Figure from the paper that illustrates the approach of probing the transition state for amyloid growth by experiments and simulations

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Dec 21

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...

Figure 1a from the paper that outlines the method. Caption: "Peptides from the N-terminal IDR of DDX4 were encoded in a DNA library for mRNA display and transcribed using purified T7 RNA polymerase. The resulting mRNA contains a ribosomal binding site (RBS), a coding sequence (CDS) for peptide of interest, and a HA-tag for purification via the translated peptide. The synthetic mRNA (pink) is ligated to a puromycin-containing PEG-linker (black) containing a DNA sequence (blue) that forms a hetero duplex with the mRNA to facilitate single stranded RNA ligation. The resulting mRNA display molecule is purified using the HA-tag and added to an excess of DDX4N1 to measure partitioning of all library members through RNA/DNA sequencing. "

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Rasmus Hartmann-Petersen @rhp-lab.bsky.social · Dec 20

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.

www.cell.com

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Nov 29

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 🧬🧶🧪

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Nov 25

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...

Flyer for the course Keeping up with the interactome - How IDPs work including a list of speakers:
Professor Tanja Mittag, St Jude Children’s Hospital, Memphis, US
Professor Kresten Lindorff-Larsen, BIO, SCIENCE, UCPH
Professor Ylva Ivarsson, Uppsala University, Sweden
Dr. Michael Wehr, Systasy Bioscience, Munich, Germany
Professor Zsuzsanna Dostztányi, Eötvös Loránd University, Hungary
Professor Kristian Strømgaard, HEALTH, UCPH
Professor Stefano Gianni, Sprienza University of Rome, Italy
Professor Per Jemth, Uppsala University, Sweden
Dr. Franziska Schöppe, Novo Nordisk A/S, Denmark
Professor Benjamin Schuler, University of Zurich, Switzerland
Professor Alfonse De Simone, University of Naples, Italy
Dr. Malene Ringkjøbing Jensen, CNRS, Grenoble, France
Alleyn Plowright, Chief Scientific Officer, Pangea Bio, London UK
Professor Birthe B. Kragelund, BIO, SCIENCE, UCPH

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Rohit V. Pappu @rohitpappu68.bsky.social · Nov 15

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

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