Big thanks to all the coauthors, especially @ma3ke.bsky.social for driving this paper forward. Really nice to have this work finally out there, and especially cool that it's part of the special issue honoring the work of David Goodsell. A huge inspiration for whole-cell modeling!

Beyond the minimal cell, we also packed the multi-compartment architecture of a mitochondrion and built an all-atom SARS-CoV-2 virion in a respiratory aerosol (based on work from the Amaro lab). Want to try it yourself? We wrote a tutorial on the Martini website, give it a go!

Building realistic models of cells means fitting proteins, RNA, and metabolites at experimental concentrations inside complex cellular architectures. Here's a movie showing how we pack the cytoplasmic space of the JCVI-Syn3A cell:

Instead of a tree, I can offer a snowman! ☃️

Built using bentopy, based on David Naranjo's idea.

The input file can be found here: gist.github.com/ma3ke/723f9c....