title: A Method for Finding Metabolic Pathways Using Atomic Group Tracking.
abstract: A fundamental computational problem in metabolic engineering is to find pathways between compounds. Pathfinding methods using atom tracking have been widely used to find biochemically relevant pathways. However, these methods require the user to define the atoms to be tracked. This may lead to failing to predict the pathways that do not conserve the user-defined atoms. In this work, we propose a pathfinding method called AGPathFinder to find biochemically relevant metabolic pathways between two given compounds. In AGPathFinder, we find alternative pathways by tracking the movement of atomic groups through metabolic networks and use combined information of reaction thermodynamics and compound similarity to guide the search towards more feasible pathways and better performance. The experimental results show that atomic group tracking enables our method to find pathways without the need of defining the atoms to be tracked, avoid hub metabolites, and obtain biochemically meaningful pathways. Our results also demonstrate that atomic group tracking, when incorporated with combined information of reaction thermodynamics and compound similarity, improves the quality of the found pathways. In most cases, the average compound inclusion accuracy and reaction inclusion accuracy for the top resulting pathways of our method are around 0.90 and 0.70, respectively, which are better than those of the existing methods. Additionally, AGPathFinder provides the information of thermodynamic feasibility and compound similarity for the resulting pathways.
authors.affiliation: School of Computer Science and Engineering, South China University of Technology, Guangzhou, China.|School of Computer, Electronics and Information, Guangxi University, Nanning, China.
authors.forename: Yiran
authors.identifier: http://orcid.org/0000-0001-6289-8766
authors.initials: Y
authors.lastname: Huang
authors.affiliation: School of Computer, Electronics and Information, Guangxi University, Nanning, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Zhong
authors.affiliation: Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.
authors.forename: Hai Xiang
authors.initials: HX
authors.lastname: Lin
authors.affiliation: School of Chemistry and Chemical Engineering, Guangxi University, Nanning, China.
authors.forename: Jianyi
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016208:Databases, Factual; D053858:Metabolic Networks and Pathways; D008956:Models, Chemical; D013816:Thermodynamics