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FMM specifications


Unique identifier OMICS_02693
Name FMM
Alternative name From Metabolite to Metabolite
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for From Metabolite to Metabolite

FMM citations


A review of computational tools for design and reconstruction of metabolic pathways

PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] ctions as vertices with the edges connecting either a substrate to a reaction or a reaction to a product. Most of the pathway design tools are based on substrate graphs, namely Pathway Hunter Tools , FMM , RouteSearch , and MRE . In contrast to the substrate graph, bipartite graph accounts for enzyme information in the vertices of reactions. Bipartite graph-based tools (such as CMPF and NeAT ) en […]


A review of parameters and heuristics for guiding metabolic pathfinding

J Cheminform
PMCID: 5602787
PMID: 29086092
DOI: 10.1186/s13321-017-0239-6

[…] re is the average of the reaction scores of all its reactions. In Faust et al. [], RPAIR mappings are used without atom tracking to show the connectivity of compounds without annotations of atoms. In FMM [], reactions are represented as a 16,884×16,884 matrix, where each row and column represents a compound and having a ‘1’ represents that there exists a forward reaction between the compounds. In […]


Mathematical modelling of clostridial acetone butanol ethanol fermentation

Appl Microbiol Biotechnol
PMCID: 5320022
PMID: 28210797
DOI: 10.1007/s00253-017-8137-4

[…] esents a unidirectional molecular flow. Its vertices (or nodes) represent signals, e.g. metabolite concentrations, and the edges (branches, arrows) represent functional dependencies, e.g. carbon flow from metabolite to metabolite (Mason ). A vertex receives signals via incoming edges and transmits information along outgoing edges, information being, for instance, increases or decreases in the conc […]


Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data

Biomed Res Int
PMCID: 4993939
PMID: 27595107
DOI: 10.1155/2016/7863706

[…] s; for example, metabolic pathways of Corynebacterium glutamicum are rationally engineered to produce L-amino acids on an industrial scale []. To accomplish this task, specific tools are used such as FMM (from metabolite to metabolite) [] Cytoscape [], CellDesigner [], SBW (Systems Biology Workbench) [], COPASI (COmplex PAthway SImulator) [], and COBRA (COnstraints Based Reconstruction and Analysi […]


In silico methods for linking genes and secondary metabolites: The way forward

PMCID: 5640692
PMID: 29062931
DOI: 10.1016/j.synbio.2016.03.001

[…] tep, potential enzymes that can catalyze each of these enzymatic reactions can be identified by sequence or structure based bioinformatics methods. In recent years few computational tools like ReBit, FMM and PathPred have been developed for retro-biosynthetic enumeration of biochemical reactions and have been applied for biosynthesis of novel natural products by synthetic biology approach. Even th […]


Development of bio based fine chemical production through synthetic bioengineering

Microb Cell Fact
PMCID: 4302092
PMID: 25494636
DOI: 10.1186/s12934-014-0173-5

[…] data [,].Once key enzymes are identified, one can move to pathway design and optimization for microbial production of the target compound. Several computational tools are available, such as BNICE [], FMM [], RetroPath [], and DESHARKY [] and M-path [] for designing de novo metabolic pathways. These resources provide different views of metabolic pathways for microbial production that are generated […]


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FMM institution(s)
Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsin-Chu, Taiwan, China

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