PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search.

ABSTRACT: Metabolic pathway design is an essential step in the course of constructing an efficient microbial cell factory to produce high value-added chemicals. Meanwhile, the computational design of biologically meaningful metabolic pathways has been attracting much attention to produce natural and non-natural products. However, there has been a lack of effective methods to perform metabolic network reduction automatically. In addition, comprehensive evaluation indexes for metabolic pathway are still relatively scarce. Here, we define a novel uniform similarity to calculate the main substrate-product pairs of known biochemical reactions, and develop further an efficient metabolic pathway design tool named PyMiner. As a result, the redundant information of general metabolic network (GMN) is eliminat

SUBMITTER: Song X 

PROVIDER: S-EPMC9000129 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature