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.
Allows users to compare enzyme reactions. EC-BLAST comprises a set of algorithms to handle reactions automatically. The software allows rapid comparisons between reactions at bond change level, reaction center level and reaction structure similarity level.
Simulates microbial degradation based on a hierarchically ordered set of principal metabolic transformations. CATABOL is a probabilistic scheme that was able to reproduce experimentally documented transformations of perfluorinated chemicals (PFCs). It can also be used for simulating catabolism and predicting biodegradation products in ready biodegradability tests. The set of transformations includes 141 abiotic and biologically mediated reactions.
Allows retrosynthetic design of metabolic pathways. RetroPath is a webserver that integrates several techniques. RetroPath workflow is a versatile reaction network tool, built to be modular enough to answer most metabolic engineering needs. The software was developed to answer the need for a tool to predict reaction networks.
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.
It can reconstruct metabolic pathways form one metabolite to another metabolite among different species, based mainly on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and other integrated biological databases.
A web-based pathway analysis platform which provides full access to the set of pathways that can be imported into a chassis organism such as Escherichia coli through the application of an Extended Metabolic Space modeling framework.
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.
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.
An efficient search algorithm based on atom mapping rules and path weighting schemes that returns relevant or textbook-like routes between a source and a product metabolite within seconds for genome-scale networks. Its speed allows the algorithm to be used interactively through a web interface to visualize relevant routes and local networks for one or multiple organisms based on data from KEGG.
A Monte Carlo algorithm that finds a metabolic pathway from a target compound by exploring a database of enzymatic reactions. DESHARKY outputs a biochemical route to the host metabolism together with its impact in the cellular context by using mathematical models of the cell resources and metabolism.
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.
Mines biochemical reaction features. RDT is an application supplying multiple characteristics such as the ability to perform atom-atom mapping (AAM) on chemical reactions catalyzed by enzymes or to generate reaction patterns or images of the mapped reactions. This program is able to mine bond changes (BCs) or reaction centres as well as to compute similarity between reactions.
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.
Predicts reactions between unknown molecules. ReactionMiner is a general and fully-automated method based on subgraph mining, which can be applied to predict novel metabolic routes in thousands of organisms. The software uses a given metabolic reaction database and the chemical structure of the participant molecules. It can be used to identify/recover biochemically preferred pathways between metabolites and predict pathways to known and novel/unused compounds.
Predicts experimentally observed polar, radical, and pericyclic reactions. ReactionPredictor is a machine learning reaction prediction system that handles expanded atom types and incorporates a mechanistic pathway search for multistep reaction prediction. The web server allows both single-step and pathway prediction.
Identifies the metabolic pathway class as well as the individual pathways to which previously unknown small molecules might be associated with. TrackSM employs information from structurally similar scaffolds to determine a metabolic class and also estimate individual pathway to which the molecule is likely to belong.. This tool is useful for finding the biochemical functions of small molecules.
Encompasses the reconstruction of a genome-scale pan-organism metabolic network. Mecat provides a helpful computational method for the directed design of biosynthetic production pathways and the planning of syntheses. The tool supplies a very useful basis for the eventual selection of pathways to be implemented in the wet lab. Users can select or define own criteria for ranking results.