Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

ABSTRACT: The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, many algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom ma

SUBMITTER: Preciat Gonzalez GA 

PROVIDER: S-EPMC5471289 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature