%0 Journal Article %1 Hadadi2015Design %A Hadadi, Noushin %A Hatzimanikatis, Vassily %D 2015 %J Current Opinion in Chemical Biology %K retrosynthesis review %P 99--104 %R 10.1016/j.cbpa.2015.06.025 %T Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways %U http://dx.doi.org/10.1016/j.cbpa.2015.06.025 %V 28 %X Retrobiosynthetic approaches enable the design of de novo pathways to target compounds. Computational tools are essential for the retrobiosynthetic design of an 'infinite' number of synthetic pathways. Pruning approaches are crucial for avoiding the risk of combinatorial explosion. Systematical classification of the de novo pathway pruning strategies are discussed. Scoring and ranking of retrosynthetic pathways are crucial for their practical implementation. 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.

@article{Hadadi2015Design, abstract = { Retrobiosynthetic approaches enable the design of de novo pathways to target compounds. Computational tools are essential for the retrobiosynthetic design of an 'infinite' number of synthetic pathways. Pruning approaches are crucial for avoiding the risk of combinatorial explosion. Systematical classification of the de novo pathway pruning strategies are discussed. Scoring and ranking of retrosynthetic pathways are crucial for their practical implementation. 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.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Hadadi, Noushin and Hatzimanikatis, Vassily}, biburl = {https://www.bibsonomy.org/bibtex/2339a77c3c5ad941b7c3e41aeed4bca59/karthikraman}, citeulike-article-id = {13675514}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.cbpa.2015.06.025}, doi = {10.1016/j.cbpa.2015.06.025}, interhash = {904e7ee945f7c83dc74aff15a3562f78}, intrahash = {339a77c3c5ad941b7c3e41aeed4bca59}, issn = {13675931}, journal = {Current Opinion in Chemical Biology}, keywords = {retrosynthesis review}, month = oct, pages = {99--104}, posted-at = {2016-07-25 09:52:21}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways}, url = {http://dx.doi.org/10.1016/j.cbpa.2015.06.025}, volume = 28, year = 2015 }