cellPACK

cellPACK is a virtual mesoscope to model and visualize structural systems biology: it packs molecular structures into cellular compartments, following curated biological recipes, to build 3D models of viruses, organelles and whole cells.

cellPACK was introduced by Johnson et al. in Nature Methods (2015), co-authored by Ludovic Autin, PhD. Ludo's Molecular Graphics Lab at Scripps Research works on cellPACK with Graham Johnson and the Allen Institute for Cell Science. Models built with cellPACK, including HIV-1 in blood serum, the blood plasma exosome and insulin secretory granules, can be explored in Mesoscope and Mesoscale Explorer.

Source code: github.com/mesoscope/cellpack
Lab website: https://autinlab.org

CellPackGPU

CellPackGPU is a GPU-accelerated version of the packing method that builds dense, realistic cytoplasmic models almost instantly. It was introduced in "Instant construction and visualization of crowded biological environments" and used to build the whole-cell structural models of Mycoplasma genitalium. The source is not yet public.

How to cite

cellPACK: Johnson GT, Autin L, Al-Alusi M, Goodsell DS, Sanner MF, Olson AJ. cellPACK: a virtual mesoscope to model and visualize structural systems biology. Nat Methods 12(1):85-91, 2015. doi:10.1038/nmeth.3204
CellPackGPU: Klein T, Autin L, Kozlikova B, Goodsell DS, Olson A, Groller ME, Viola I. Instant construction and visualization of crowded biological environments. IEEE Trans Vis Comput Graph 24(1):862-872, 2018. doi:10.1109/TVCG.2017.2744258
Mycoplasma models: Maritan M, Autin L, Karr J, Covert MW, Olson AJ, Goodsell DS. Building structural models of a whole mycoplasma cell. J Mol Biol 434(2):167351, 2022. doi:10.1016/j.jmb.2021.167351

Ludo's Molecular Graphics Lab · Scripps Research · La Jolla, CA · autin@scripps.edu