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Metabolic pathway prediction

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…
EC-BLAST
Web

EC-BLAST

Allows users to compare enzyme reactions. EC-BLAST comprises a set of…

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,…

RetroPath
Web
Desktop

RetroPath

Allows retrosynthetic design of metabolic pathways. RetroPath is a webserver…

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…

Pathway Hunter…
Web

Pathway Hunter Tool

Allows users to reconstruct and dynamically visualize biochemical pathways…

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…

MRE
Web

MRE Metabolic Route Explorer

Ranks biosynthesis routes from the perspective of the integration of new…

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.…

SensiPath
Web
Desktop

SensiPath

Assists the design of sensing-enabling metabolic pathways (SEMPs). SensiPath is…

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…

FMM
Web

FMM From Metabolite to Metabolite

It can reconstruct metabolic pathways form one metabolite to another metabolite…

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…

MetaRoute
Web

MetaRoute

An efficient search algorithm based on atom mapping rules and path weighting…

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…

Mecat
Desktop

Mecat

Encompasses the reconstruction of a genome-scale pan-organism metabolic…

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…

CarbonSearch
Desktop

CarbonSearch

Finds metabolic pathways. CarbonSearch implements algorithms that uses atom…

Finds metabolic pathways. CarbonSearch implements algorithms that uses atom tracking to identify linear pathways and find branched metabolic pathways.

XTMS
Web

XTMS

A web-based pathway analysis platform which provides full access to the set of…

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…

ReactionMiner
Desktop

ReactionMiner

Predicts reactions between unknown molecules. ReactionMiner is a general and…

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…

M-path
Web

M-path

A computational platform, M-path, to explore synthetic metabolic pathways…

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…

ReactionPredict…
Web

ReactionPredictor

Predicts experimentally observed polar, radical, and pericyclic reactions.…

Predicts experimentally observed polar, radical, and pericyclic reactions. ReactionPredictor is a machine learning reaction prediction system that handles expanded atom types and incorporates a…

MetaHype
Web

MetaHype

Enumerates pathways for target compounds in KEGG. MetaHype is a web server for…

Enumerates pathways for target compounds in KEGG. MetaHype is a web server for enumeration of pathway leading to the production of a desired compound.

Metabolic…
Web

Metabolic tinker

Aims to guide the design of synthetic metabolic pathways between any two…

Aims to guide the design of synthetic metabolic pathways between any two desired compounds.

Desharky
Desktop

Desharky

A Monte Carlo algorithm that finds a metabolic pathway from a target compound…

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…

BNICE
Web

BNICE Biochemical Network Integrated Computational Explorer

Identifies possible biochemical reaction from a given set of enzyme reaction.…

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…

Rahnuma
Web

Rahnuma

A versatile tool that can be used for many different applications including…

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…

MRSD
Web

MRSD Metabolic Route Search and Design

A tool to search and design routes based on the weighted compound transform…

A tool to search and design routes based on the weighted compound transform diagraph.

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