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UM-PPS specifications


Unique identifier OMICS_22541
Alternative name University of Minnesota pathway prediction system
Interface Web user interface
Restrictions to use None
Programming languages Java, Perl
Computer skills Basic
Stability No
Maintained No


This tool is not available anymore.

Publication for University of Minnesota pathway prediction system

UM-PPS in publications

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

[…] 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 single […]

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

[…] (m) ; (iv) route designer applies a similar rule to that of rdm, by defining reaction core and extended reaction core with primary and secondary bonds and non-reacting neighborhood atoms ; (v) um-pps and gem-path use smirks and smarts, which exploit a feature string encoding the chemical properties of each atom. reactions operators generally loose information while converting a known […]

PMCID: 4938425
PMID: 27390860
DOI: 10.1371/journal.pone.0158896

[…] of known signal transduction pathways and their functional annotations in the form of association rules. there are also tools that predict biodegradation pathways such as meta ([], catabol [] and um-pps []. in addition, relative reasoning has been used for the prediction of mammalian detoxification pathways in order to limit combinatorial explosion []. association rule mining was used in [] […]

PMCID: 3694648
PMID: 23812977
DOI: 10.1093/bioinformatics/btt244

[…] necessary between the source and target compounds. many of the prediction systems based on this framework are not freely available (; ; ), but there are some free web servers such as pathpred () and university of minnesota pathway prediction system (umpps; ). a serious limitation of the compound-filling framework is that it is not suitable for predicting pathways for many compounds at a time […]

PMCID: 3351732
PMID: 22587916
DOI: 10.1186/2042-5783-2-1

[…] also been used to develop a computational metabolic pathway prediction system that can be applied to chemicals for which biodegradation data is currently lacking. the um-pathway prediction system (um-pps) relies on metabolic rules that are based on organic functional groups and predicts plausible biodegradative metabolism. the predictions are useful to environmental chemists that look […]

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UM-PPS institution(s)
Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA; Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, Zürich, Switzerland; Swiss Federal Institute for Aquatic Science and Technology (Eawag), Dubendorf, Switzerland; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
UM-PPS funding source(s)
Supported by U.S. National Science Foundation (NSF9630427); Swiss National Science Foundation (PA002-113140); Lhasa Limited; the Minnesota Supercomputing Institute.

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