Protein biophysicist working on intrinsically disordered proteins in neuroscience and biotech. Assoc. prof at @MolBiolAU and @PromemoAU. (He/Him)
Magnus Kjærgaard
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This project was part of an industrial PhD program of Nathalie Wyss conducted in collaboration with Novo Nordisk, where Charlotte Wiberg was co-supervisor for the whole journey!
IDPSeminars is back for a final seminar of spring 2026!
This week, we welcome Wenwei Zheng and Sigrid Milles! The seminar is at 10 AM PST / 1 pm EST / 7 PM European time on Thursday. Sign up via our website at idpseminars.com!
Magnus Kjærgaard
How should we model and fit bivalent binding in biosensor assays? Current models don't work well, so we made a new one and used it to study the spatial tolerance of avidity in antibodies.
www.cell.com/biophysj/abs...
We developed a new model for bivalent binding in biosensor assays (SPR, BLI, GCI ... ) based on the competition between different bound forms.
The key advantage is in how it describes the increase in the fast dissociation phase at high analyte concentrations.
To get a "clean" data set for modelling and study the spatial dependence of avidity in bivalent binding of antibodies, Nathalie developed a set of protein nanocalipers by concatenating coiled-coils based on work in link below
www.nature.com/articles/s41...
The model provides a modest improvement in fit and a more mechanistically meaningful evolution in modeled species.
Caveat: Many fitting parameters. You need really good data, and probably also some parameter constrains.
Do you want to study the stability of a designed protein that doesn't unfold below 90 ºC 🔥? Combine a denaturant and temperature and then analyse the results with our newest tool: CheMelt 🧪
Online:
- spc.embl-hamburg.de/app/chemelt
As Docker image (faster):
- hub.docker.com/r/emblspc/ch...
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-...
IDPSeminars
Magnus Kjærgaard
Magnus Kjærgaard
Magnus Kjærgaard
Magnus Kjærgaard
Video
Osvaldo Burastero
Kresten Lindorff-Larsen
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📝
Kresten Lindorff-Larsen
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/...
Kresten Lindorff-Larsen
AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level https://www.biorxiv.org/content/10.1101/2025.10.19.683306v1
