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Metabolizer

Metabolizer enumerates the metabolites of a given substrate with the reactions of the given biotransformation library and calculates their estimated probabilities of formation and accumulation. Metabolite prediction provides ideas about the metabolic fate of molecules. Biodegradation deactivates drugs, activates pro-drugs and metabolites can have biological effects which may mean risk for living organs. Knowing metabolic fate early can help drug designers to improve the metabolic stability of compounds or to avoid toxicity risks. Metabolizer's knowedge base is stored in biotransformation libraries. A library contains a set of generic reactions, rules to make transformations selective, examples, literature references ranking and some other data. Biotransformation libraries can be "plugged in" easily, and you can even create and use your own ones. A human xenobiotic phase I biotransformation library is built-in the application, however, for immediate use.

Options

Biotransformation library: Though, Metabolizer is shipped with a buit-in biotransformation library by default, it is possible to load your own custom library even for predicting the metabolites of other species (i.e. bacterial, plant, mammal, rat).
Exclude condition: Metabolites fulfilling this Chemical Terms expression are ignored.
Termination condition: Metabolites fulfilling this Chemical Terms expression are not enumerated further.
Range Options: Metabolites with high global accumulation values are considered likely.
Enumeration mode: Exhaustive enumeration method producing minor metabolites as well.
Fast mode limit: When not in exhaustive mode, metabolites below this relative formation, are ignored, value 10 means 10% of the highest rate from the same parent compound.
Filter alternative routes and calculate global indicators: Filter alternative routes and calculate global indicators.
Global accummulation filter: Return metabolites with higher global accumulation than this value.
Global number filter: Return the given number of metabolites in their global accumulation order.
Output type: Generate molecule for metabolite output, reaction for biotransformation output.
Generation limit: The maximum number of generations.
Population limit: The maximum number of metabolites, when reached further generations are not enumerated.
Structure column: The substrate column.

Input Ports

: Input table that contains substrate structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

: Output table that contains metabolic molecules or reactions in Marvin format.

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Installation

To use this node in KNIME, install the extension ChemAxon/Infocom JChem Extensions Feature from the below update site following our NodePit Product and Node Installation Guide:

v4.2

A zipped version of the software site can be downloaded here.

Plugin provider: Infocom Corporation

Plugin version: 4.0.0.v192100

On NodePit since: 2020-07-13

Last update: 2025-02-04

Tags: Streamable

KNIME versions: From v4.0 to v4.2

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