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DESHARKY: Automatic design of metabolic pathways for ...

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DESHARKY: Automatic design of metabolic pathways for optimal cell growth. ... (DESHARKY) that finds a metabolic pathway from a target compound by exploring a database of enzymatic reactions ...

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DESHARKY: automatic design of metabolic pathways for ...

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9/5/2008 · DESHARKY: automatic design of metabolic pathways for optimal cell growth ... Alfonso Jaramillo; DESHARKY: automatic design of metabolic pathways for optimal cell growth, Bioinformatics, Volume 24, Issue 21, 1 November 2008, Pages 2554–2556, https ... and also taking advantage of databases of Gibbs free energies for all enzymatic reactions ...

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MRE: a web tool to suggest foreign enzymes for the ...

MRE: a web tool to suggest foreign enzymes for the ...

4/29/2016 · DESHARKY Free download E. coli KEGG reactions No Growth rate Source or target compound, EC numbers for enzymes, genes for some foreign enzymes, growth rate reduction measures BNICE Closed access No host Predicted reactions No No pathway ranking 3-level EC number for each predicted chemical transformation

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(PDF) MRE: a web tool to suggest foreign enzymes for the ...

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MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

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Enzyme annotation for orphan and novel reactions using ...

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4/9/2019 · Recent advances in synthetic biochemistry have resulted in a wealth of novel hypothetical enzymatic reactions that are not matched to protein-encoding genes, deeming them “orphan.” A large number of known metabolic enzymes are also orphan, leaving important gaps in metabolic network maps. Proposing genes for the catalysis of orphan reactions is critical for applications ranging from ...

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Design of computational retrobiosynthesis tools for the ...

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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 ...

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Computational tools for the synthetic design of ...

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1/23/2012 · Synthetic biology approaches for the de novo design of biosynthetic pathways have developed rapidly in recent years. Takano and colleagues …

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A review of computational tools for design and ...

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A generalized pathway design workflow highlighting the five steps is presented in Fig. 1: (1) database construction, (2) metabolic network representation, (3) network pruning, (4) search algorithm implementation, and (5) pathway ranking to select the best pathways of interest.In the following section, we discuss a number of pathway design algorithms that follow this design workflow (see Table ...

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3/28/2010 · There have been several methods developed for the prediction of synthetic metabolic pathways leading to the production of desired chemicals. In these approaches, novel pathways were predicted based on chemical structure changes, enzymatic information, and/or reaction mechanisms, but the approaches generating a huge number of predicted results are difficult to be applied to real …

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An overview of pathway prediction tools for synthetic ...

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We previously reported [12] the need for integration of various disciplines and use of computational tools for DNA synthesis in microbial strain improvement. 2.3. DESHARKY This pathway prediction system is based on enzymatic reactions, but it approaches the search in a way that is unique among the aforementioned systems.

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Summary: SynBioSS (Synthetic Biology Software Suite) is a suite of software for the modeling and simulation of synthetic genetic constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to …

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The present invention relates to a method and system for dynamically analyzing, determining, predicting and displaying ranked suitable heterologous biosynthesis pathways for a specified host. The present invention addresses the problem of finding suitable pathways for the endogenous metabolism of a host organism because the efficacy of heterologous biosynthesis is affected by competing ...

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A retrosynthetic biology approach to metabolic pathway ...

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8/5/2011 · Synthetic biology is used to develop cell factories for production of chemicals by constructively importing heterologous pathways into industrial microorganisms. In this work we present a retrosynthetic approach to the production of therapeutics with the goal of developing an in situ drug delivery device in host cells. Retrosynthesis, a concept originally proposed for synthetic chemistry ...

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3/1/2019 · Successfully designed and implemented plant-specific synthetic metabolic pathways hold promise to increase crop yield and nutritional value. Advances in synthetic biology have already demonstrated the capacity to design artificial biological pathways whose behavior can be predicted and controlled in microbial systems. However, the transfer of these advances to model plants and crops …

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4/27/2014 · Millions of toxic chemicals have been produced for use in a variety of industries [].These chemicals have often been released into the environment due to anthropogenic activities, where they contaminate soil and water [].Furthermore, many chemicals persist in the environment, causing severe problems to living organisms; accordingly, it is crucial that these compounds be removed from the ...

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7/28/2006 · We give algorithms for finding the k shortest paths (not required to be simple) connecting a pair of vertices in a digraph. Our algorithms output an implicit representation of these paths in a digraph with n vertices and m edges, in time O(m + n log n + k).

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Designing overall stoichiometric conversions and ...

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11/4/2015 · Using a depth-first search, variations of the k-shortest path approach have been used to design and classify pathways based on their length 36, negativity of free energy change for each reaction ...

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The increasing need for the bio-based industrial production of compounds via microbial cell factories leads to a demand for computational pathway prediction tools. A variety of algorithms have been developed that can be used to identify possible metabolic pathways and their corresponding enzymatic parts. These prediction tools play a central role in metabolic pathway design and microbial ...

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Integration of bioinformatics to biodegradation

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Integration of bioinformatics to biodegradation. Pankaj Kumar Arora 1 and Hanhong ... BNICE screens out all possible pathways for thermodynamic feasibility based on the Gibbs free energies of the reaction and selects feasible ... Carrera J, Prather KJ, Jaramillo A. DESHARKY: automatic design of metabolic pathways for optimal cell growth. ...

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3/1/2016 · Shifting from chemical to biotechnological processes is one of the cornerstones of 21st century industry. The production of a great range of chemicals via biotechnological means is a key challenge on the way toward a bio-based economy. However, this shift is occurring at a pace slower than initially expected. The development of efficient cell factories that allow for competitive production ...

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Biocatalysis has become a powerful tool for the synthesis of high-value compounds, particularly so in the case of highly functionalized and/or stereoactive products. Nature has supplied thousands of enzymes and assembled them into numerous metabolic pathways. Although these native pathways can be use to produce natural bioproducts, there are many valuable and useful compounds that have no ...

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4/1/2015 · Motivation: The urgent need for efficient and sustainable biological production of fuels and high-value chemicals has elicited a wave of in silico techniques for identifying promising novel pathways to these compounds in large putative metabolic networks. To date, these approaches have primarily ...

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Bioinformatics 2014 Sep 14;30(17):2508-10. Epub 2014 May 14. Institute of Systems and Synthetic Biology, CNRS - Université d'Évry Val d'Essonne, F-91000 Évry, France and School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom Institute of Systems and Synthetic Biology, CNRS - Université d'Évry Val d'Essonne, F-91000 Évry, France and School of Life Sciences ...

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