Matteo Cagiada
@mcagiada.bsky.social
🇮🇹, Computational biophysicist, Postdoc in #PRISM at #LinderstrømLang Centre for Protein Science (KLL group) @uni_copenhagen
Hi Pierre! Thank you for your message! I have put this in my TO DO list for a revised version of the datasets (probably around review time). We had pretty compressed archives to fit zenodo limits, so I would check if zip compression can do it. I will update you when is live!
November 13, 2025 at 10:24 PM
Hi Pierre! Thank you for your message! I have put this in my TO DO list for a revised version of the datasets (probably around review time). We had pretty compressed archives to fit zenodo limits, so I would check if zip compression can do it. I will update you when is live!
Find all the details and links to the databases in the preprint manuscript (doi.org/10.1101/2025...)
Uncovering the flexibility of CDR loops in antibodies and TCRs through large-scale molecular dynamics
Antibody structures are composed of framework regions that adopt a conserved fold and complementarity determining regions (CDR) loops which are far more variable. Flexibility of CDR loops has been lin...
doi.org
November 12, 2025 at 9:21 PM
Find all the details and links to the databases in the preprint manuscript (doi.org/10.1101/2025...)
FlAbDab and FTCRDab are open-access datasets designed for reuse, extension and community benchmarking. We’d love to hear from you if you build on them.
November 12, 2025 at 9:21 PM
FlAbDab and FTCRDab are open-access datasets designed for reuse, extension and community benchmarking. We’d love to hear from you if you build on them.
Built on our customised CALVADOS 3 setup, they comprise CG simulations of >150,000 antibody and T-cell receptor systems, and reproduce ensemble metrics from all-atom and experimental data.
November 12, 2025 at 9:21 PM
Built on our customised CALVADOS 3 setup, they comprise CG simulations of >150,000 antibody and T-cell receptor systems, and reproduce ensemble metrics from all-atom and experimental data.
A huge thanks to @sokrypton.org for key contributions, and to Charlotte Deane (@opig.stats.ox.ac.uk) and @lindorfflarsen.bsky.social for their invaluable guidance and support.
April 17, 2025 at 11:34 PM
A huge thanks to @sokrypton.org for key contributions, and to Charlotte Deane (@opig.stats.ox.ac.uk) and @lindorfflarsen.bsky.social for their invaluable guidance and support.
If you want to hear more about this project, you can join me on June 26 at the next 39th Annual Symposium of The Protein Society (San Francisco), where I will present the results of this work!
March 27, 2025 at 4:44 PM
If you want to hear more about this project, you can join me on June 26 at the next 39th Annual Symposium of The Protein Society (San Francisco), where I will present the results of this work!
Many thanks to @sokrypton.org and @lindorfflarsen.bsky.social for their help and mentorship during this project!.
March 27, 2025 at 4:44 PM
Many thanks to @sokrypton.org and @lindorfflarsen.bsky.social for their help and mentorship during this project!.
As Kresten mentioned, the only way to install specific pytorch dependencies at the moment is to restart the kernel after installing a new version on Miniconda. I will add a warning at the top, so the next user will know! Thanks for the tip @msuskiewicz.bsky.social !
December 17, 2024 at 11:55 PM
As Kresten mentioned, the only way to install specific pytorch dependencies at the moment is to restart the kernel after installing a new version on Miniconda. I will add a warning at the top, so the next user will know! Thanks for the tip @msuskiewicz.bsky.social !