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XTMS specifications


Unique identifier OMICS_04776
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for XTMS

XTMS citations


Pathway design using de novo steps through uncharted biochemical spaces

Nat Commun
PMCID: 5766603
PMID: 29330441
DOI: 10.1038/s41467-017-02362-x

[…] ges, or molecule fingerprint changes between substrates and products have been encoded as reaction rule operators in formats such as BEM, RDM, and SMIRKS. Pathway prediction techniques such as BNICE, XTMS, UM-PPS, PathPred, Route Designer, and GEM-Path employ reaction rule operators for a single molecular target iteratively in a retrosynthetic fashion so as to identify a bioconversion from a singl […]


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

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

[…] hesis of commodity chemicals, biofuels, or pharmaceuticals, but have also been applied to develop biosensing pathways for target molecules. For example, Libis et al. used the retrosynthetic approach (XTMS) to identify pathways from undetectable target molecules such as drugs, pollutants, and biomarkers to known inducer molecules, which could then activate transcription factors . The activated tran […]


A review of parameters and heuristics for guiding metabolic pathfinding

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

[…] ility, among other factors (such as binding site covalence and chemical similarity). The XTMS webserver [] uses a scoring function to rank pathway results found by the RetroPath search algorithm. The XTMS scoring function incorporates the thermodynamic favorability of a pathway by both including the sum of all the ΔG values (taken from MetaCyc) of each reaction in a pathway and including the numbe […]


Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle

PMCID: 5063057
PMID: 27185383
DOI: 10.1039/c6np00018e

[…] y efficiency have been proposed. For instance, Metabolic Tinker prioritizes pathways based on thermodynamic feasibility; FindPath in addition considers pathway length and theoretical yield; RetroPath/XTMS, scores enzyme performance based on predicted promiscuous activities and adds toxicity of intermediates to the ranking; and GEM-Path includes flux efficiency.An important consideration when desig […]


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XTMS institution(s)
University of Evry, iSSB, Evry, France; CNRS, iSSB, Evry, France; IISER Mohali, SAS Nagar, Manauli, Mohali, Punjab, India

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