Fig. 1.

Overview of the design and functionality of ssbio. Underlined fixed-width text indicates added functionality to COBRApy for a genome-scale model loaded using ssbio. (A) A simplified schematic showing the addition of a Protein to the core objects of COBRApy (non-underlined fixed-width text). A gene is directly associated with a protein, which can act as a monomeric enzyme or form an active complex with itself or other proteins (the asterisk denotes that methods for complexes are currently under development). (B) Summary of functions available for computing properties on a protein sequence or structure. (C) Uses of a GEM-PRO, from the bottom-up and the top-down. Once all protein sequences and structures are mapped to a genome-scale model, the resulting GEM-PRO has uses in multiple areas of study, as noted in the main text