Paper Info
Title
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model.
Abstract
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 http://design.rxnfinder.org/novopathfinder/.
Year
DOI
Venue
2020
10.1093/nar/gkaa230
NUCLEIC ACIDS RESEARCH
DocType
Volume
Issue
Journal
48
W1
ISSN
Citations 
PageRank 
0305-1048
0
0.34
References 
Authors
0
11
Name
Order
Citations
PageRank
Shaozhen Ding102.03
Yu Tian24919.62
Pengli Cai301.69
Dachuan Zhang401.69
Xingxiang Cheng501.01
Dandan Sun601.01
Le Yuan701.69
Junni Chen801.69
Weizhong Tu901.69
Dong-Qing Wei1010.70
Qian-Nan Hu11264.80