HMFF comes with Mosaic, a software ecosystem for membrane segmentation, refinement, HMFF simulations, and morphometrics. (6/n) 🔗https://github.com/KosinskiLab/mosaic

For example, it allows building models like this filamentous influenza A virion ⬇️ (5/n)

HMFF aids in on-membrane particle picking, supports multiscale modeling, and allows backmapping to atomic detail (4/n)

This enables physically realistic and complete membrane models of cells, organelles, and viruses, consistent with experimental data (3/n)

Helfrich Monte Carlo Flexible Fitting (HMFF) optimizes membrane models directly in electron microscopy densities (2/n)

New method toward modeling cells and viruses! HMFF enables integrative membrane modeling and simulation guided by electron microscopy data. Created by Valentin Maurer and Marc Siggel @embl.org ‪‪@cssbhamburg.bsky.social‬, in collaboration with @WPezeshkian lab (1/n) www.biorxiv.org/content/10.1...

We captured a snapshot of in-cell protein contact sites during influenza A virus infection. In-cell crosslinking, AlphaFold modeling, and functional follow-ups revealed new host factors and mechanisms. A step toward modeling the infected cell.

Sorry Albert, I can't have coffee with you today because time is relative, and mine just ran out. #chatgpt4o

Draw a ribbon representation of a protein structure shaped like a banana, with alpha-helices, beta-sheets, and loops clearly visible, maintaining realistic molecular geometry and coloring styles typical for protein visualizations.

Perhaps this is not the only time this picture will be shown during a Nobel Prize lecture 😉

By the way, seeds are your friends when running AlphaFold 3. I use at least 20 by default.

We have released version 2 of AlphaPulldown - a general pipeline for high-throughput structural modeling!
Software: github.com/KosinskiLab/...
Preprint: biorxiv.org/content/10.1...

Crosslinks can sometimes improve AlphaFold3 models. Crosslinking is an experimental method often used as a source of distance restraints in modeling. In AlphaFold3, instead of using restraints, crosslinks can be included as covalent ligands. Thanks to Agnieszka Obarska-Kosinska for the idea.