Kresten Lindorff-Larsen
@lindorfflarsen.bsky.social
Protein and coffee lover, father of two, professor of biophysics and sudo scientist at the Linderstrøm-Lang Centre for Protein Science, University of Copenhagen 🇩🇰
Pinned
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/...
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/...
Reposted by Kresten Lindorff-Larsen
TTPD Episode 9 with @fraserlab.com: I Can Do It With a Broken Grant Cycle
(Sorry for the crappy audio in places!)
Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools
wankowiczlab.com/2025/11/24/T...
(Sorry for the crappy audio in places!)
Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools
wankowiczlab.com/2025/11/24/T...
November 24, 2025 at 3:22 PM
TTPD Episode 9 with @fraserlab.com: I Can Do It With a Broken Grant Cycle
(Sorry for the crappy audio in places!)
Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools
wankowiczlab.com/2025/11/24/T...
(Sorry for the crappy audio in places!)
Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools
wankowiczlab.com/2025/11/24/T...
Reposted by Kresten Lindorff-Larsen
Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.
November 23, 2025 at 11:18 PM
Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.
One of these is Figure 1 from my first paper and the other is an image generated using Nano Banana Pro solely from the caption of Figure 1 of my first paper
![[Figure generated using AI] Progress curves for the reaction between GSH (Merck) and 2-VP (Aldrich). 0.2 mM 2-VP was incubated with 5 mM (circles), 10 mM (squares), 15 mM (diamonds), and 20 mM (triangles) GSH at pH 6.8, and 25°C. At the indicated times, 20 l were withdrawn and injected into a Vydac C18 column on a Hewlett–Packard HPLC system running at 1 ml/min with 0.1% trifluoroacetic acid in 10% acetonitrile. The reaction could be followed using online fluorescence detection ( ex 254 nm, em 340 nm), since free 2-VP fluoresces much more that its GSH conjugate. The solid lines represent nonlinear least-squares fit to a single exponential function. (Inset) Pseudo-first-order rate constants are plotted against glutathione concentration. The slope of the straight line is an estimate of the second-order rate constant at pH 6.8.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:av5rwmfzfvex2hquvjxtlqlz/bafkreicvkeu6oucxhtcjppmro3xl4k7io6dkgvspiqfnjhm2ad34lt52am@jpeg)
![[Figure from my first paper with the caption] Progress curves for the reaction between GSH (Merck) and 2-VP (Aldrich). 0.2 mM 2-VP was incubated with 5 mM (circles), 10 mM (squares), 15 mM (diamonds), and 20 mM (triangles) GSH at pH 6.8, and 25°C. At the indicated times, 20 l were withdrawn and injected into a Vydac C18 column on a Hewlett–Packard HPLC system running at 1 ml/min with 0.1% trifluoroacetic acid in 10% acetonitrile. The reaction could be followed using online fluorescence detection ( ex 254 nm, em 340 nm), since free 2-VP fluoresces much more that its GSH conjugate. The solid lines representnonlinear least-squares fit to a single exponential function. (Inset) Pseudo-first-order rate constants are plotted against glutathione concentration. The slope of the straight line is an estimate of the second-order rate constant at pH 6.8.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:av5rwmfzfvex2hquvjxtlqlz/bafkreiesuag34bsz45mfvir6fxrotzs6dqn5kss4mlygacwumgm4odtl6y@jpeg)
November 23, 2025 at 9:18 PM
One of these is Figure 1 from my first paper and the other is an image generated using Nano Banana Pro solely from the caption of Figure 1 of my first paper
Reposted by Kresten Lindorff-Larsen
Italian researchers (and Batman) conducted a field study on the Milan metro (138 rides)... ⬇️
"Passengers were significantly more likely to offer their seat when Batman was present (67.21% vs. 37.66%, OR = 3.393, p < 0.001)"
I can smell IgNobel
pmc.ncbi.nlm.nih.gov/articles/PMC...
"Passengers were significantly more likely to offer their seat when Batman was present (67.21% vs. 37.66%, OR = 3.393, p < 0.001)"
I can smell IgNobel
pmc.ncbi.nlm.nih.gov/articles/PMC...
a close up of a cartoon character wearing a batman costume .
ALT: a close up of a cartoon character wearing a batman costume .
media.tenor.com
November 23, 2025 at 5:24 PM
Italian researchers (and Batman) conducted a field study on the Milan metro (138 rides)... ⬇️
"Passengers were significantly more likely to offer their seat when Batman was present (67.21% vs. 37.66%, OR = 3.393, p < 0.001)"
I can smell IgNobel
pmc.ncbi.nlm.nih.gov/articles/PMC...
"Passengers were significantly more likely to offer their seat when Batman was present (67.21% vs. 37.66%, OR = 3.393, p < 0.001)"
I can smell IgNobel
pmc.ncbi.nlm.nih.gov/articles/PMC...
Reposted by Kresten Lindorff-Larsen
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 19, 2025 at 9:16 PM
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
Reposted by Kresten Lindorff-Larsen
Jeg står her omkring i morgen fra ca. kl 10 og frem til 11:30 eller der omkring. Så går turen videre til Panum. Håber vi ses!
November 16, 2025 at 7:53 PM
Jeg står her omkring i morgen fra ca. kl 10 og frem til 11:30 eller der omkring. Så går turen videre til Panum. Håber vi ses!
Reposted by Kresten Lindorff-Larsen
Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1
November 13, 2025 at 1:47 AM
Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1
Reposted by Kresten Lindorff-Larsen
Since you ask.
From the birth of quantum to the birth of CERN.
From the birth of quantum to the birth of CERN.
November 13, 2025 at 12:43 PM
Since you ask.
From the birth of quantum to the birth of CERN.
From the birth of quantum to the birth of CERN.
Reposted by Kresten Lindorff-Larsen
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.
November 12, 2025 at 9:21 PM
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.
😱 I worry the next step is to allow spaces in filenames
No no no begs every archivist. You are never going to be able to find anything. Please don’t start using emojis in file names. Who asked for this? What fresh hell is next?
November 12, 2025 at 8:21 PM
😱 I worry the next step is to allow spaces in filenames
Reposted by Kresten Lindorff-Larsen
Uncovering the flexibility of CDR loops in antibodies and TCRs through large-scale molecular dynamics https://www.biorxiv.org/content/10.1101/2025.11.10.687725v1
November 12, 2025 at 7:48 PM
Uncovering the flexibility of CDR loops in antibodies and TCRs through large-scale molecular dynamics https://www.biorxiv.org/content/10.1101/2025.11.10.687725v1
Reposted by Kresten Lindorff-Larsen
Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...
November 5, 2025 at 4:23 PM
Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...
Reposted by Kresten Lindorff-Larsen
🎙️ Next up Dec 2 in VESS!
Thea Schulze (Lindorff-Larsen Lab): Predicting mutated protein abundance @tkschulze.bsky.social
Taylor Mighell (Lehner Lab): Massive mutagenesis to understand GPCRs @taylor-mighell.bsky.social
🔗 More info at varianteffect.org/seminar-series
@varianteffect.bsky.social
Thea Schulze (Lindorff-Larsen Lab): Predicting mutated protein abundance @tkschulze.bsky.social
Taylor Mighell (Lehner Lab): Massive mutagenesis to understand GPCRs @taylor-mighell.bsky.social
🔗 More info at varianteffect.org/seminar-series
@varianteffect.bsky.social
November 4, 2025 at 6:31 PM
🎙️ Next up Dec 2 in VESS!
Thea Schulze (Lindorff-Larsen Lab): Predicting mutated protein abundance @tkschulze.bsky.social
Taylor Mighell (Lehner Lab): Massive mutagenesis to understand GPCRs @taylor-mighell.bsky.social
🔗 More info at varianteffect.org/seminar-series
@varianteffect.bsky.social
Thea Schulze (Lindorff-Larsen Lab): Predicting mutated protein abundance @tkschulze.bsky.social
Taylor Mighell (Lehner Lab): Massive mutagenesis to understand GPCRs @taylor-mighell.bsky.social
🔗 More info at varianteffect.org/seminar-series
@varianteffect.bsky.social
Reposted by Kresten Lindorff-Larsen
*If you would like to be considered for a talk at this workshop, please register & submit an abstract by 7 November*
We also have a fantastic line-up of invited speakers: Matteo Degiacomi, Lucie Delemotte, Weria Pezeshkian, Mohsen Sadeghi & Ilpo Vattulainen
Registration: aias.au.dk/events/show/...
We also have a fantastic line-up of invited speakers: Matteo Degiacomi, Lucie Delemotte, Weria Pezeshkian, Mohsen Sadeghi & Ilpo Vattulainen
Registration: aias.au.dk/events/show/...
November 4, 2025 at 11:46 AM
*If you would like to be considered for a talk at this workshop, please register & submit an abstract by 7 November*
We also have a fantastic line-up of invited speakers: Matteo Degiacomi, Lucie Delemotte, Weria Pezeshkian, Mohsen Sadeghi & Ilpo Vattulainen
Registration: aias.au.dk/events/show/...
We also have a fantastic line-up of invited speakers: Matteo Degiacomi, Lucie Delemotte, Weria Pezeshkian, Mohsen Sadeghi & Ilpo Vattulainen
Registration: aias.au.dk/events/show/...
Reposted by Kresten Lindorff-Larsen
Probing the energy landscape of α-Synuclein amyloid fibril formation by systematic K-to-Q mutagenesis https://www.biorxiv.org/content/10.1101/2025.11.01.685997v1
November 3, 2025 at 10:48 PM
Probing the energy landscape of α-Synuclein amyloid fibril formation by systematic K-to-Q mutagenesis https://www.biorxiv.org/content/10.1101/2025.11.01.685997v1
Reposted by Kresten Lindorff-Larsen
Anyway, we need some joy, so here's the Egyptian foreign minister being given a Lego Pyramid by the Danish foreign minister.
November 3, 2025 at 2:35 PM
Anyway, we need some joy, so here's the Egyptian foreign minister being given a Lego Pyramid by the Danish foreign minister.
I’m excited to be speaking at the AI in Science Summit 2025 in my home town of Copenhagen #AIS25 #AI4Science
I will be speaking about how AI and biophysics can come together to study protein dynamics
I will be speaking about how AI and biophysics can come together to study protein dynamics
November 3, 2025 at 8:09 AM
I’m excited to be speaking at the AI in Science Summit 2025 in my home town of Copenhagen #AIS25 #AI4Science
I will be speaking about how AI and biophysics can come together to study protein dynamics
I will be speaking about how AI and biophysics can come together to study protein dynamics
Reposted by Kresten Lindorff-Larsen
🔬 CECAM Workshop: “Integrative and Multiscale Modelling Approaches to Illuminate CryoEM/ET Data”
Join us in Toulouse, 24–26 March 2026, to explore how molecular simulations, AI tools, can be integrated to cryo-EM and cryo-ET data.
🧬 Selection: brief CV + motivation letter required.
Apply 👇
Join us in Toulouse, 24–26 March 2026, to explore how molecular simulations, AI tools, can be integrated to cryo-EM and cryo-ET data.
🧬 Selection: brief CV + motivation letter required.
Apply 👇
CECAM - Integrative and Multiscale Modelling Approaches to Illuminate CryoEM/ET data
www.cecam.org
November 1, 2025 at 9:47 AM
🔬 CECAM Workshop: “Integrative and Multiscale Modelling Approaches to Illuminate CryoEM/ET Data”
Join us in Toulouse, 24–26 March 2026, to explore how molecular simulations, AI tools, can be integrated to cryo-EM and cryo-ET data.
🧬 Selection: brief CV + motivation letter required.
Apply 👇
Join us in Toulouse, 24–26 March 2026, to explore how molecular simulations, AI tools, can be integrated to cryo-EM and cryo-ET data.
🧬 Selection: brief CV + motivation letter required.
Apply 👇
Reposted by Kresten Lindorff-Larsen
Quantum computers - what are they and how will they change things?
Have a listen/watch here: @timcoulson.bsky.social and I chat with Ian Walmsley, newly appointed director of the Oxford Quantum Institute: The Science and Promise of Quantum Computing
youtu.be/sPTyvBKJruU
Have a listen/watch here: @timcoulson.bsky.social and I chat with Ian Walmsley, newly appointed director of the Oxford Quantum Institute: The Science and Promise of Quantum Computing
youtu.be/sPTyvBKJruU
Science Of The Times Ep 29_Entangled Futures: The Science and Promise of Quantum Computing
YouTube video by Science Of The Times Podcast
youtu.be
November 1, 2025 at 8:24 AM
Quantum computers - what are they and how will they change things?
Have a listen/watch here: @timcoulson.bsky.social and I chat with Ian Walmsley, newly appointed director of the Oxford Quantum Institute: The Science and Promise of Quantum Computing
youtu.be/sPTyvBKJruU
Have a listen/watch here: @timcoulson.bsky.social and I chat with Ian Walmsley, newly appointed director of the Oxford Quantum Institute: The Science and Promise of Quantum Computing
youtu.be/sPTyvBKJruU
Reposted by Kresten Lindorff-Larsen
Where Parisians post their preprints…
October 31, 2025 at 6:28 PM
Where Parisians post their preprints…
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE
Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods
doi.org/10.1093/bioi...
Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods
doi.org/10.1093/bioi...
October 29, 2025 at 7:45 AM
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE
Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods
doi.org/10.1093/bioi...
Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods
doi.org/10.1093/bioi...
Not just #YAAFC
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 9:54 PM
Not just #YAAFC
I attended a summer school on Spetses 🇬🇷 just as I was beginning my PhD. Looks like I will be going again in 2026 with "Lost in Integration vol. 2". Details to follow.
October 28, 2025 at 9:22 PM
I attended a summer school on Spetses 🇬🇷 just as I was beginning my PhD. Looks like I will be going again in 2026 with "Lost in Integration vol. 2". Details to follow.
New review on experimental datasets that can be used to benchmark protein force fields. And if that doesn’t tickle your fancy, the data can also be used to benchmark machine learning models for biomolecular structure and dynamics.
In the latest @livecomsjournal.bsky.social
perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!:
livecomsjournal.org/index.php/li...
#compchem
perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!:
livecomsjournal.org/index.php/li...
#compchem
October 28, 2025 at 3:51 PM
New review on experimental datasets that can be used to benchmark protein force fields. And if that doesn’t tickle your fancy, the data can also be used to benchmark machine learning models for biomolecular structure and dynamics.
Reposted by Kresten Lindorff-Larsen
Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...
GitHub - aqlaboratory/openfold-3: OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3
OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 - aqlaboratory/openfold-3
github.com
October 28, 2025 at 9:30 AM
Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...