An interactive, three-dimensional visual structural systems biology reconstruction of a whole E. coli cell
No complete, three-dimensional reconstruction of a prokaryote-scale cell exists to represent proteomic, metabolomic, and genomic data in an accessible manner. With the availability of experimental and computational information on the structures, stoichiometry, and localization of cellular components of Escherichia coli, along with the development of visualization tools such as cellPACK and chromosome simulation models, we have the “ingredients” we need to put together a model for the well-studied organism. This project integrates this data into an interactive, three-dimensional structural biology model of an E. coli cell for modern web browsers. The cell model contains still structural representations of the proteins, protein complexes, cell membrane, and chromosome, and is built on a pipeline that can produce a similar model from different data. It can be used as a stepping stone for organizing the information available on E. coli and as a stepping stone to develop models for other organisms at the prokaryotic and eukaryotic scales.