iiinova — where your digital self keeps evolving

Reposted by Alok Bharadwaj

Arjen Jakobi @cryotud.bsky.social · 06/10/2026

State-selective nanobodies to probe Guanylate-binding protein coat assembly and function Lennart & Tanja identified and validated conformation-selective nanobodies to probe and interfere w/ GBP coat formation on intracellular bacteria. Led by @lpagani.bsky.social. www.biorxiv.org/content/10.6...

1123

Reposted by Alok Bharadwaj

Lennart Pagani @lpagani.bsky.social · 07/10/2026

Check out our new preprint! We describe conformation-specific nanobodies that allow us to study Guanylate-binding proteins and target different stages of their assembly. We shed some new light on current models and hypotheses!

092

Reposted by Alok Bharadwaj

Structural Biology @actacrystd.iucr.org · 06/08/2026

August issue is out! journals.iucr.org/d/issues/202... The cover highlights SURFER, a lightweight GPU-accelerated extension for UCSF ChimeraX that enables rapid semantic differentiation of membrane or membrane-mimic density from macromolecular signal in cryo-EM maps. More at doi.org/10.1107/S205...

0177

Reposted by Alok Bharadwaj

Arjen Jakobi @cryotud.bsky.social · 20/07/2026

The LocScale 2.0 and SURFER papers are now both published in final form. LocScale 2.0: www.nature.com/articles/s41... SURFER: onlinelibrary.wiley.com/iucr/doi/10.... Led by @alok-bharadwaj.bsky.social with contributions of former MSc/Bsc students Reinier de Bruin and Lotte Veerbeek.

03811

Reposted by Alok Bharadwaj

Arjen Jakobi @cryotud.bsky.social · 27/02/2026

New preprint by @alok-bharadwaj.bsky.social explaining the workings of SURFER, a simple tool to segment membrane, micelle or nanodisc densities in cryoEM maps. Try it via the @chimerax.ucsf.edu ToolShed: cxtoolshed.rbvi.ucsf.edu/apps/chimera... Despite LocScale in the name, it works on any map.

0228

Reposted by Alok Bharadwaj

Arjen Jakobi @cryotud.bsky.social · 15/09/2025

We finally wrote up the paper for LocScale-2.0. edu.nl/pvhxv Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps. Code: cryotud.github.io/locscale/ Work by @alok-bharadwaj.bsky.social and Reinier.

03315

Reposted by Alok Bharadwaj

Arjen Jakobi @cryotud.bsky.social · 22/05/2025

Want to try LocScale-2.0 without installing locally? Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud. edu.nl/ur3ge

0145

Reposted by Alok Bharadwaj

Arjen Jakobi @cryotud.bsky.social · 22/05/2025

We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation. Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation. cryotud.github.io/locscale/

112238