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Reactions_​with_​RDKit_​Hub_​MarvinSketch

Reactions with RDKit

This workflow demonstrates the one and two component reaction nodes from the RDKit community extension. This worklfow demonstrates the functionality of the One and Two Component Reaction nodes from the RDKit extension. The One Component reaction is using one reactant, the Two Component reaction is using two reactants. The reaction is given as RXN.

This workflow version uses the MarvinSketch node to draw the reaction and is suitable for ChemAxon license holders.

Do a "reverse reaction" on themolecules Split for the resulting amines and acids andfilter each for duplicates Second reaction with eachamide and acid fraction Check if the reaction product is in the original data set and indicate the result in a separate column This worklfow demonstrates the functionality of the One and Two Component Reaction nodes from the RDKit extension. The One Component reaction is using one reactant, theTwo Component reaction is using two reactants. The reaction is given as RXN. Note: As of December 2020 the MarvinSketch will not be freely available anymore. This workflow version is meant for users with a ChemAxon license. The input data has been taken from the supplementary of this open access publication: https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.9b01658 fragment moleculedraw reaction 1draw reaction 2Compound analogues from publicationacidsamines RDKit Canon SMILES RDKit One ComponentReaction MarvinSketch Row Splitter MarvinSketch RDKit Two ComponentReaction RDKit From Molecule File Reader Reference RowSplitter DuplicateRow Filter RDKit Canon SMILES DuplicateRow Filter DuplicateRow Filter RDKit DescriptorCalculation ConstantValue Column ConstantValue Column Concatenate Column Resorter Visualize molecularproperties Renderer to Image Do a "reverse reaction" on themolecules Split for the resulting amines and acids andfilter each for duplicates Second reaction with eachamide and acid fraction Check if the reaction product is in the original data set and indicate the result in a separate column This worklfow demonstrates the functionality of the One and Two Component Reaction nodes from the RDKit extension. The One Component reaction is using one reactant, theTwo Component reaction is using two reactants. The reaction is given as RXN. Note: As of December 2020 the MarvinSketch will not be freely available anymore. This workflow version is meant for users with a ChemAxon license. The input data has been taken from the supplementary of this open access publication: https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.9b01658 fragment moleculedraw reaction 1draw reaction 2Compound analogues from publicationacidsamines RDKit Canon SMILES RDKit One ComponentReaction MarvinSketch Row Splitter MarvinSketch RDKit Two ComponentReaction RDKit From Molecule File Reader Reference RowSplitter DuplicateRow Filter RDKit Canon SMILES DuplicateRow Filter DuplicateRow Filter RDKit DescriptorCalculation ConstantValue Column ConstantValue Column Concatenate Column Resorter Visualize molecularproperties Renderer to Image

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: alice.krebs
Created at: 2020-11-13
On NodePit since: 2021-01-18
Last update: 2026-01-07
Created with KNIME version: v4.3.0
Tags: Life SciencesCheminformaticsComputational ChemistryRDKit

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