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Metabolic pathway detection software tools | Metabolic engineering data analysis

Construction of synthetic metabolic pathways promises sustainable production of diverse chemicals and materials. In order to design synthetic metabolic pathways of high value, computational methods are needed to expand present knowledge by mining comprehensive chemical and enzymatic information databases.

Source text:
(Araki et al., 2015) M-path: a compass for navigating potential metabolic pathways. Bioinformatics.

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Pathway Hunter Tool
Allows users to reconstruct and dynamically visualize biochemical pathways using shortest path. Pathway Hunter Tool is a “Network Biology” tool that identifies enzymes for potential drug targets and designs synthetic networks with highly specialized metabolic functions. The web server provides three features: Shortest Path Analysis, Load Points & Choke Points Analysis and Statistical Analysis. Users can choose organism(s) as model(s) or build their own or build their own virtual organism.
Assists the design of sensing-enabling metabolic pathways (SEMPs). SensiPath is a web-based tool that aims to enlarge the number of detectable compounds for synthetic biology applications. The software provides synthetic biologists with new solutions to build circuits having the ability of triggering a genetic response when a compound of interest is present. It can serve users wishing to perform cell-mediated detection of a compound when no direct-sensing solution is feasible.
MRE / Metabolic Route Explorer
Ranks biosynthesis routes from the perspective of the integration of new reactions into an endogenous metabolic system, for a given pair of starting and desired compounds in a given chassis organism. MRE suggests, for each heterologous biosynthesis pathway, actual enzymes for foreign metabolic reactions. It also generates information on competing endogenous reactions for the consumption of metabolites. These chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle.
Transform-MinER / Transforming Molecules in Enzyme Reactions
Transforms query substrate molecules into products by applying known enzyme reactions at potential reaction centres (RCs) and retrieves the most similar native enzyme reactions for each. Transform-MinER is a web application that (1) identifies potential RCs in query substrates, (2) calculates the RC molecular environment (MolEnv) similarity in query and native substrates for generating rank ordered lists; and (3) applies transformations to produce products. It can be useful to identify substrates that may show promiscuous activity with enzymes.
A computational platform, M-path, to explore synthetic metabolic pathways including putative enzymatic reactions and compounds. M-path is an iterative random algorithm which makes efficient use of chemical and enzymatic databases to find potential synthetic metabolic pathways. M-path can readily control the search space, and perform well compared to exhaustively enumerating possible pathways. A web-based pathway viewer is also developed to check extensive metabolic pathways with evaluation scores on the basis of chemical similarities.
BNICE / Biochemical Network Integrated Computational Explorer
Identifies possible biochemical reaction from a given set of enzyme reaction. BNICE is a computational framework that can address the synthesis problem in metabolic pathways. The software can be applied to a large number of different systems of biotechnological importance. Application of the framework allows the identification of every possible chemical compound that can be produced by the generalized enzyme reactions in these pathways.
A versatile tool that can be used for many different applications including predicting catabolic or biosynthetic pathways, identifying knock-out targets that may compromise pathway function and comparing pathways and reactions at different levels of a phylogeny. Rahnuma can also be used to compare metabolic networks in distantly related, but metabolically linked organisms such as hosts and symbionts. The unique features of this tool, which allow the users to answer specific biological questions, distinguish it from currently available tools and are likely to prove useful to both experimental biologists and bioinformaticians, who will be able to use Rahnuma to test and develop hypotheses and to explore and interpret experimental results.
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