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.
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.
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.
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.
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.
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.
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 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.