Efficient searching and annotation of metabolic networks using chemical similarity

Pertusi, Dante A.; Stine, Andrew; Broadbelt, Linda J.; Tyo, Keith E.J.

doi:10.1093/bioinformatics/btu760

Cited by 48 publications

(46 citation statements)

References 50 publications

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“…Having a known target creates an opportunity to utilize a retrosynthetic strategy for developing an efficient reaction network for its production. Computational tools exist for finding such reaction networks in biological systems with one example being a program called Biological Network Integrated Computational Explorer (BNICE) . This program utilizes an automated reaction network generation (NetGen) approach to design synthetic pathways using reaction rules curated from biochemical reaction databases for identifying potential biological retrosynthetic pathways to a target molecule (see bottom of Figure ).…”

Section: Bioprivileged Molecule Conceptmentioning

confidence: 99%

“…Computational tools exist for finding such reactionn etworks in biological systems with one example being aprogram called Biological Network Integrated Computational Explorer (BNICE). [10,11] This program utilizes an automated reactionn etwork generation (NetGen) [12] approach to design synthetic pathways using reaction rules curated from biochemical reaction databases for identifying potential biological retrosynthetic pathways to at arget molecule (see bottom of Figure 1). Once the possible biological pathwaysh ave been identified, the DBTL cycle can be utilized to develop an organism capable of synthesizing adipic acid.…”

Section: Bioprivileged Molecule Conceptmentioning

confidence: 99%

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A Robust Strategy for Sustainable Organic Chemicals Utilizing Bioprivileged Molecules

Shanks

Broadbelt

2019

ChemSusChem

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Biobased chemicals will inevitably be an important part of a sustainable organic chemical industry. Current efforts in biobased chemicals are largely driven by opportunistic chemical product targets requiring complete technology development from feedstock to final product for a specific molecule. To enhance the development of biobased chemicals, it is important to create strategies that can be more systematic and can leverage advancements across multiple final products. Discussed here is the concept of bioprivileged molecules, which are chemical intermediates that have the potential to be efficiently converted into a range of product molecules that can both directly replace existing petrochemicals and are novel molecules that impart enhanced performance properties in end‐use applications.

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Section: Bioprivileged Molecule Conceptmentioning

confidence: 99%

Section: Bioprivileged Molecule Conceptmentioning

confidence: 99%

A Robust Strategy for Sustainable Organic Chemicals Utilizing Bioprivileged Molecules

Shanks

Broadbelt

2019

ChemSusChem

Self Cite

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“…The complications that arise from the huge number of generated pathways resulting in the existing pathway enumeration methods has been previously discussed [14,39,44] and solutions have been proposed to enumerate 'a set of viable pathways' based on predefined criteria, rather than all possible pathways.…”

Section: Qualitative Pruning In the Pathway Enumeration Stepmentioning

confidence: 99%

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

Hadadi

Hatzimanikatis

2015

Current Opinion in Chemical Biology

118

106

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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 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.

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“…Pathway prediction algorithms map substrate/product pairs to enzymatic activities and then to genes [45,46]. Metabolism enumeration algorithms can be used to find novel reactions that are not yet catalogued in biochemical databases [47].…”

Section: Introductionmentioning

confidence: 99%

Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets

Barupal

Fan

Fiehn

2018

Current Opinion in Biotechnology

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Access to high quality metabolomics data has become a routine component for biological studies. However, interpreting those datasets in biological contexts remains a challenge, especially because many identified metabolites are not found in biochemical pathway databases. Starting from statistical analyses, a range of new tools are available, including metabolite set enrichment analysis, pathway and network visualization, pathway prediction, biochemical databases and text mining. Integrating these approaches into comprehensive and unbiased interpretations must carefully consider both caveats of the metabolomics dataset itself as well as the structure and properties of the biological study design. Special considerations need to be taken when adopting approaches from genomics for use in metabolomics. R and Python programming language are enabling an easier exchange of diverse tools to deploy integrated workflows. This review summarizes the key ideas and latest developments in regards to these approaches.

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Efficient searching and annotation of metabolic networks using chemical similarity

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 48 publications

References 50 publications

A Robust Strategy for Sustainable Organic Chemicals Utilizing Bioprivileged Molecules

A Robust Strategy for Sustainable Organic Chemicals Utilizing Bioprivileged Molecules

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets

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