DGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.

ABSTRACT: Group contribution (GC) methods are conventionally used in thermodynamics analysis of metabolic pathways to estimate the standard Gibbs energy change (ΔrG'o) of enzymatic reactions from limited experimental measurements. However, these methods are limited by their dependence on manually curated groups and inability to capture stereochemical information, leading to low reaction coverage. Herein, we introduce an automated molecular fingerprint-based thermodynamic analysis tool called dGPredictor that enables the consideration of stereochemistry within metabolite structures and thus increases reaction coverage. dGPredictor has comparable prediction accuracy compared to existing GC methods and can capture Gibbs energy changes for isomerase and transferase reactions, which exhibit no overall gr

SUBMITTER: Wang L 

PROVIDER: S-EPMC8496854 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature