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Publication for XTMS
Pathway design using de novo steps through uncharted biochemical spaces
[…] 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
[…] 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
[…] 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
[…] 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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