title: Ab initio reconstruction of metabolic pathways.
abstract: We propose a new formulation for the problem of ab initio metabolic pathway reconstruction. Given a set of biochemical reactions together with their substrates and products, we consider the reactions as transfers of atoms between the chemical compounds and we look for successions of reactions transferring a maximal (or preset) number of atoms between a given source and sink compound. We state this problem as the one of finding a composition of partial injections that maximizes the image size. First, we study the theoretical complexity of this problem, state some related problems and then give a practical algorithm to solve them. Finally, we present two applications of this approach to the reconstruction of the tryptophan biosynthesis pathway and to the glycolysis.
authors.affiliation: LSR-IMAG, Saint Martin d'Hères Cedex, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Boyer
authors.forename: Alain
authors.initials: A
authors.lastname: Viari
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D008954:Models, Biological; D008956:Models, Chemical; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D020543:Proteome