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.
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.
Allows for the creation of networks composed of metabolic relationships, protein and protein-DNA interactions. BioNetBuilder is a plugin for Cytoscape that permits associations from comparative genomics regardless of what database the gene product originally came from or what data format the integration databases support. It does not require a rigid database schema, file-format or data-model that new data sources must conform to.
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.
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.
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.