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Tautomer Generator (Naomi)

This node takes any given input molecule and enumerates all reasonable protomers and tautomers for it at physiological pH. It is based on the Naomi software library developed in partnership between the University of Hamburg (ZBH) and BioSolveIT. As a community service, it is provided free of charge.

Options

Molecule column: Name of the molecule column.
Generation type: Choose neutralize, tautomers or protomers including tautomers.
Append all data columns of the library table: Select this if you want to append all data columns of your input table to the output table.
Keep debug files and show the log after the run: This setting keeps all temporary files and opens an editor to show the output of the external program. This setting is very helpful for debugging.

Input Ports

: Library: Input table with molecules in sdf, smiles or mol2 format.

Output Ports

: Results: Tautomers and protomers or neutralized versions of the input molecules. The molecule type corresponds to the input molecules.
: Errors: Rows of the incoming table containing molecules which could not be processed for any reason.

Popular Predecessors

Generate 3D Coordinates21 %
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Popular Successors

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Installation

To use this node in KNIME, install the extension BioSolveIT Naomi for Knime from the below update site following our NodePit Product and Node Installation Guide:

v5.2

Plugin provider: BioSolveIT GmbH

Plugin version: 2.29.3.202309291626

On NodePit since: 2023-12-06

Last update: 2026-01-01

KNIME versions: From v3.6 to v5.2

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