Fig. 4
Workflow for generating simulation-ready models of all proteins in metabolism. a The first stage involves mapping the genes of the organism to available crystallographic and NMR protein structures, found in the Protein Data Bank (PDB). The second stage performs homology modeling for genes without available structures. The third stage performs ranking and filtering of structures and homology models for each gene based on set selection criteria (e.g., SSI, Sres and Scomp). These criteria refer to a scoring metric that ranks a PDB structure based on sequence identity (SSI), resolution (Sres), or homology model based on the similarity in secondary structure composition (Scomp) compared to the structure. As shown in b, evaluation of the sequence identity between the protein structure sequence and that of the wild-type sequence and PDB resolution (in Å) allows filtering of low-quality structures. In the final stage, all high quality PDB files that require minimal modification (e.g., reversion of the sequence to match that of the wild-type) are further refined, as depicted in (c)