novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
Artikel i vetenskaplig tidskrift, 2020

To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at


Shaozhen Ding

Chinese Academy of Sciences

Yu Tian

Wuhan University of Technology

Pengli Cai

Chinese Academy of Sciences

Dachuan Zhang

Chinese Academy of Sciences

Xingxiang Cheng

Chinese Academy of Sciences

Dandan Sun

Chinese Academy of Sciences

Le Yuan

Chalmers, Biologi och bioteknik, Systembiologi

Junni Chen

Wuhan LifeSynther Science and Technology Co. Limited

Weizhong Tu

Wuhan LifeSynther Science and Technology Co. Limited

Dong Qing Wei

Shanghai Jiao Tong University

Qian Nan Hu

Chinese Academy of Sciences

Nucleic Acids Research

0305-1048 (ISSN) 1362-4962 (eISSN)

Vol. 48 W1 W477-W487


Teoretisk kemi

Biokatalys och enzymteknik

Organisk kemi





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