PathPred specifications

Information


Unique identifier OMICS_03569
Name PathPred
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kae Morishima <>

Publication for PathPred

PathPred in publications

 (13)
PMCID: 5906575
PMID: 29706937
DOI: 10.3389/fmicb.2018.00672

[…] by those grown on chca, as compared to the other na and to glucose., rhodococcus aetherivorans bcp1 genome analysis was performed to detect the possible genes involved in na degradation. using pathpred software and in silico comparative analyses, we identified genes encoding cyclohexanone monooxygenases and genes possibly encoding enzymes involved in oxidative degradation processes […]

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

[…] 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 single source. […]

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

[…] bond-electron matrix (bem) to define non-bonded valence electrons and bond orders ; (ii) xtms uses a molecular signature to generate reaction rules based on substructure of adjacent atoms ; (iii) pathpred uses the rdm pattern (developed by kegg researchers) consisting of reaction center atom (r), atoms of different region (d), and atoms of the matched region (m) ; (iv) route designer applies […]

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

[…] vectors that describe difference in number of atom/bond feature types between substrates and products. in cho et al. [], there is a reaction rules database containing constructed reaction rules. pathpred [] uses so-called rdm patterns from rpairs, which take into account the reaction center, the difference regions, and the matched regions between the reactants and products. pathpred also […]

PMCID: 4980782
PMID: 27510651
DOI: 10.1186/s12920-016-0205-6

[…] the names of the enzymes catalyzing the reactions., the next step in pathway annotation was to determine the synthesis pathway from fragments to drug compound. to accomplish this task, we used the pathpred webserver (http://www.genome.jp/tools/pathpred), which predicts the synthesis pathway given the substrates and the final product. the pathpred webserver is linked to the kegg database […]


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PathPred institution(s)
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan

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