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Julian Streit

@julianstreit.bsky.social
84 followers 67 following 8 posts

Postdoctoral researcher in computational structural biology at the University of Copenhagen with Kresten Lindorff-Larsen

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Reposted by Julian Streit
Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
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Joe Greener @jgreener64.bsky.social · 18/09/2026
Our Garnet paper is now out in final form: a protein and small molecule force field trained from scratch, with competitive results for binding free energy prediction. pubs.rsc.org/sc/article/d...
pubs.rsc.org
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 04/09/2026
EMBO Practical Course Integrative modelling of biomolecular interactions 26 – 30 April 2027 | Athens, Greece Great speakers/teachers (and organizers 😊) Registration Deadline: 8 November 2026 meetings.embo.org/event/27-bio...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 28/08/2026
New paper on the role of disorder in peroxisome proliferator-activated receptors and the functional consequences of transient IDR–DBD interactions by Milena Lalic, Elisabeth Thomsen, @bbkrage.bsky.social and many good colleagues (w. simulations by @emilthomasen.bsky.social) doi.org/10.1038/s414...
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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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Joe Greener @jgreener64.bsky.social · 28/07/2026
Now out as a perspective in PLOS Biology. Where next for structural bioinformatics? journals.plos.org/plosbiology/...
journals.plos.org
Where next for structural bioinformatics?
Structural bioinformatics aims to answer biological questions by considering biomolecular structures at scale. This Perspective argues that now that we have accurate predictions, we need to ask what w...
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Ivana Bukvin @ivanabukvin.bsky.social · 27/07/2026
Very happy to share a new preprint characterising the unfolded state of a folding-competent domain at the cusp of folding initiation on the ribosome. Co-led by @julianstreit.bsky.social from my PhD in John Christodoulou's lab. Many thanks to all the co-authors!
biorxiv.org
The initiation of de novo protein folding on the ribosome
How the earliest structure within the unfolded state is formed during biosynthesis on the ribosome and whether it has any consequences for downstream folding remain open questions. Here, we combine 15...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 10/07/2026
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
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Caitie McCafferty @computingcaitie.bsky.social · 22/06/2026
Happy to finally share that I will be starting my independent group at the @fmiscience.bsky.social in Feb 2027 in a vibrant new environment. We will use integrative in situ structural cell biology methods to investigate ciliary structure and dynamics in several model (and non-model 👀) systems!!
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Nature Structural & Molecular Biology @natsmb.nature.com · 16/06/2026
New online: Structures of protein folding intermediates on the ribosome
dlvr.it
Structures of protein folding intermediates on the ribosome
Nature Structural & Molecular Biology, Published online: 16 June 2026; doi:10.1038/s41594-026-01814-7Atomistic structural ensembles of protein folding intermediates on the ribosome are resolved by comprehensive 19F nuclear magnetic resonance analyses integrated with molecular dynamics simulations, providing insights into cotranslational folding pathways.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 16/06/2026
Blog post by Kamil Tamiola about our joint paper on On-the-fly Probability Enhanced Sampling in the multithermal ensemble to simulate IDPs idps.substack.com/p/a-disorder... Paper: doi.org/10.1038/s414... @julianstreit.bsky.social @invemichele.bsky.social & Sandro Bottaro
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Sammy Chan @sammyhschan.bsky.social · 16/06/2026
Now in Nature SMB: how do proteins fold while still being made? We solved all-atom structures of two ribosome-tethered folding intermediates—invisible to cryo-EM, seen only by ¹⁹F NMR. Thank you @julianstreit.bsky.social, John Christodoulou & co-authors! nature.com/articles/s41594-026-01814-7
nature.com
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...
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Julian Streit @julianstreit.bsky.social · 16/06/2026
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.
nature.com
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...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21/05/2026
Another banger
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 15/05/2026
Why is it so difficult to predict accurate mutational effects on protein stability? We explored the contribution from changes in native state configurational entropy in this paper, which also happens to be the last from my PhD. A short thread of why this matters. 1/n doi.org/10.48550/arX...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 13/05/2026
If you missed the preprint, now is a good time to read the journal version of @grocklin.bsky.social et al’s fantastic paper on multiplexed HDX measurements Large-scale discovery, analysis and design of protein energy landscapes doi.org/10.1038/s415...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21/04/2026
New preprint in which we built and simulated full-length models of α-Synuclein fibrils to reveal how the fuzzy coat mediates selective binding of peptides to amyloid fibrils Work led by Carlos Pintado-Grima in a nice collaboration with Salvador Ventura's lab doi.org/10.64898/202...
Figures shows full-length fibril model after building N- and C-terminal disordered segments for each chain, yielding a fuzzy coat
surrounding the cross-β core. The figure also shows a structure representing the interaction of LL-37 peptides with the fuzzy coat (yellow peptides) and the core (pink peptides)
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Caitie McCafferty @computingcaitie.bsky.social · 08/04/2026
I am excited to share our most recent work collaborating with @centriolelab.bsky.social and @stearnslab.bsky.social to look at the ciliary base of mammalian multiciliated cells w/ cryo-ET, XL/MS, and U-ExM www.biorxiv.org/content/10.6...
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Sjors Scheres @sjorsscheres.bsky.social · 02/04/2026
Our latest @biorxivpreprint.bsky.social: "Prion-like transmission of human tau strains in the mouse brain" 🥳 With Michel Goedert and Masato Hasegawa. www.biorxiv.org/content/10.6...
biorxiv.org
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21/03/2026
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
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Joe Greener @jgreener64.bsky.social · 18/03/2026
Check out our pre-print, where we train a protein and small molecule force field from scratch with a graph neural network. We show comparable performance to existing, manually-tuned force fields on a range of tasks including binding free energy prediction. (1/4) arxiv.org/abs/2603.16770
arxiv.org
Training a force field for proteins and small molecules from scratch
Force fields for molecular dynamics are usually developed manually, limiting their transferability and making systematic exploration of functional forms challenging. We developed a graph neural networ...
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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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Michal Kolář @mhko.bsky.social · 12/03/2026
Our recent investigation of the constriction in the bacterial ribosomal tunnel is online. Unbiased all-atom MD simulations of the entire ribosome and PDB analysis show, how flexible the constriction is. The flexibility is modulated by short nascent polypetides.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 22/02/2026
Looking forward to present our work on predicting protein side-chain rotamer distributions with AlphaFold2 Monday 8:30 at #bps0226 But you should also consider instead going to the The Future of Biophysics Symposium at 9:15 to hear Giulio Tesei talk about his work on data-driven modelling of IDPs
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 16/02/2026
Happy to share our newest preprint on Parkin missense variants in work led by Erna Sol & @vvouts.bsky.social in @rhp-lab.bsky.social Using a multiplexed assay we determined the effects of 9,212 out of 9,300 single amino acid substitutions and nonsense Parkin variants. 1/n doi.org/10.64898/202...
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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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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 05/02/2026
New 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...
Probing interactions with a double mutant cycle
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 05/02/2026
Check out our newest preprint on how the chaperone BAG6 and E3 ligase RNF126 cooperate to target unstable and misfolded missense variants for degradation. Work led by Line Pedersen in @rhp-lab.bsky.social doi.org/10.64898/202...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 28/01/2026
New preprint led by Fan Cao & Giulio Tesei We present a data-driven “stickiness” scale for amino acids in intrinsically disordered proteins 🍝, learned from SAXS data on 115 proteins. The scale captures effective residue interactions without conflating size and strength doi.org/10.64898/202...
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Michele Invernizzi @invemichele.bsky.social · 21/01/2026
Sampling IDPs is tough, but can be worth the effort! OPES multithermal made it a little easier for us, hopefully you'll find it useful as well
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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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Innis Lab @innislab.bsky.social · 17/01/2026
We’re thrilled to share our latest iTP-seq protocol for mapping bacterial translation landscapes in vitro — with a complete experimental workflow streamlined by Mélanie Gillard and an open source Python library for data analysis developed by Thibaud Renault.
rdcu.be
iTP-seq: a scalable profiling workflow to characterize bacterial translation landscapes in vitro
Nature Protocols - This protocol describes inverse toeprinting coupled to next-generation sequencing, an in vitro approach to characterize bacterial translation at codon resolution that can...
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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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David Balchin @davidbalchin.bsky.social · 12/01/2026
If anyone is interested in making bacterial ribosome-nascent chain complexes and studying them using HDX-MS, we have written up a detailed protocol. rdcu.be/eYFx4 Characterise the conformational dynamics of the ribosome, nascent polypeptide and bound chaperones, label-free and at peptide-level
rdcu.be
Client Challenge
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 16/12/2025
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📝
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 09/12/2025
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...
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Gabriel Rocklin @grocklin.bsky.social · 19/11/2025
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
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David Balchin @davidbalchin.bsky.social · 14/11/2025
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...
nature.com
GroEL/ES chaperonin unfolds then encapsulates a nascent protein on the ribosome - Nature Communications
The GroEL/ES chaperonin can act during protein synthesis to promote folding. Here, Roeselová et al. show how GroEL captures, remodels and sequesters nascent proteins in its central chamber, while they...
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Matteo Cagiada @mcagiada.bsky.social · 12/11/2025
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.
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Paul Robustelli @paulrobustelli.bsky.social · 10/10/2025
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
rdcu.be
Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution
Nature Communications - This study demonstrates how to combine molecular dynamics computer simulations with experimental biophysical data to determine accurate atomic-resolution ensembles of...
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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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Chris Waudby @chriswaudby.bsky.social · 24/09/2025
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... 🧲🧪
doi.org
Kinetic NMR screening: rapidly quantifying fast ligand dissociation in fragment mixtures using ¹⁹F relaxation dispersion
Ligand-observed NMR is a key tool for detecting weak protein-ligand interactions, but translating binding signals into meaningful affinity measurements remains difficult, limiting the ability to rank ...
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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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Julian Streit @julianstreit.bsky.social · 28/06/2025
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
biorxiv.org
Protein Dynamics at Different Timescales Unlock Access to Hidden Post-Translational Modification Sites
Post-translational modifications (PTMs) alter the proteome in response to intra- and extracellular signals, providing fundamental information processing in development, homeostasis and disease. Here, ...
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Julian Streit @julianstreit.bsky.social · 25/06/2025
Now published in Advanced Science: our latest study combining NMR and MD to investigate a transient folding intermediate of human lysozyme #nmrchat #compchem
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Janet Kumita @jrkumita.bsky.social · 25/06/2025
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/...
advanced.onlinelibrary.wiley.com
Amyloid Forming Human Lysozyme Intermediates are Stabilized by Non‐Native Amide‐π Interactions
Mutational variants of human lysozyme cause fatal systemic amyloidosis by depositing kilograms of protein in the viscera of patients. Central to this process is a partially unfolded protein intermedi....
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Wojciech Kopec @wojciechkopec.bsky.social · 22/05/2025
www.qmul.ac.uk/media/news/2...
qmul.ac.uk
Electrophysiology at atomic resolution: scientists simulate ion channel currents with unprecedented accuracy
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Stephanie Wankowicz @stephanieaw.bsky.social · 16/05/2025
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
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 15/05/2025
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/...
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