title: Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways.
abstract: Designing putative metabolic pathways is of great interest in synthetic biology. Retrobiosynthesis is a discipline that involves the design, evaluation, and optimization of de novo biosynthetic pathways for the production of high-value compounds and drugs from renewable resources and natural or engineered enzymes. The best candidate pathways are then engineered within a metabolic network of microorganisms that serve as synthetic platforms for synthetic biology. The complexity of biological chemistry and metabolism requires computational approaches to explore the full possibilities of engineering synthetic pathways towards target compounds. Herein, we discuss recent developments in the design of computational tools for retrosynthetic biochemistry and outline the workflow and design elements for such tools.
authors.affiliation: Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015, Switzerland.
authors.forename: Noushin
authors.initials: N
authors.lastname: Hadadi
authors.affiliation: Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015, Switzerland. Electronic address: vassily.hatzimanikatis@epfl.ch.
authors.forename: Vassily
authors.initials: V
authors.lastname: Hatzimanikatis
mesh_terms: D000818:Animals; D053898:Biosynthetic Pathways; D003198:Computer Simulation; D006801:Humans; D008954:Models, Biological; D058615:Synthetic Biology / Q000379:methods*; D049490:Systems Biology / Q000379:methods*