This directory contains the complete composition description for the Martini model of the Minimal Cell JCVI-syn3A.
The initial version of this whole-cell model is published in Stevens et al., 2023. We treat this GitHub page as a living description of our in silico cell, which will be kept up-to-date as the cell model is further developed.
The model information is stored in the composition file, while references to the used -omics data, Martini parameters and Software tools are presented below.
- Genomics: GenBank CP016816.2
- Lipidomics: Thornburg et al., 2021
- Proteomics: Thornburg et al., 2021
- Metabolomics: Thornburg et al., 2021
- Cytosolic Protein structures: Bianchi et al., 2022
- Membrane Protein structures: PDB ids 1POY, 2XZB, 5WS4, 6BVG, 5JKI
- Ribosome structure: PDB id 4V42 and model from Uusitalo et al, 2017
- Martini Version 2.1: Marrink et al., 2007
- Proteins / amino acids: Monticelli et al., 2008
- Lipids: Wassenaar et al, 2015
- DNA: Uusitalo et al, 2015
- RNA: Uusitalo et al, 2017
- Nucleotide Cofactors and Metabolites: Sousa et al., 2021