R-group Decomposition

R-group decomposition is a special kind of substructure search that aims at finding a central structure - scaffold - and identify its ligands at certain attachment positions. The query molecule consists of the scaffold and ligand attachment points represented by R-groups.

Options

Query structure column
The query structure column.
Target structure column
The target structure column.
Undefined R-atom matches
Set the matching behavior of an undefined R atom in the query.
Bridging R-groups is allowed, different R-atoms can match the same group
Bridging R-groups is allowed, different R-atoms can match the same group.
Require undefined R-atoms with the same R-group ID should match the same structure
Require undefined R-atoms with the same R-group ID should match the same structure.
Query modification
Modify query structure by setting the option.
Attachment symbol on ligands
Set the attachment symbols.
Keep coordinates of structures
Keep coordinates of structures (otherwise align for 2D output).
Generate Markush output
Generate Markush output.
Process all hits
Process all hits.
Hit ordering
Hit ordering type for undefined R-atom atom-group matches.

Input Ports

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

Output Ports

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Output table that contains search result structure 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:

v5.9

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

Plugin provider: Infocom Corporation
Plugin version: 4.7.0.v250304
On NodePit since: 2025-12-17
Last update: 2026-01-19
KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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