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Pharmacophores Viewer

This Node Is Deprecated — This version of the node has been replaced with a new and improved version. The old version is kept for backwards-compatibility, but for all new workflows we suggest to use the version linked below.

Node to view pharmacophores in a web browser

Each pharmacophore can optionally have a ligand and/or protein.

When view is opened then it will automatically open a web browser with the viewer.

Source code available at Github.

Options

Column with pharmacophores: Column with PHAR formatted pharmacophores.
Column with labels (*): Column with labels, if no column is selected uses Row ID.
Column with ligand molecules (*): Column with SDF or Mol2 formatted molecules, if no column is selected no ligands will be shown.
Column with protein molecules (*): Column with PDB or Mol2 formatted molecules, if the pdb contain protein/ligand complex then the protein and ligand are shown, if no column is selected no proteins will be shown.
Column with transformation matrix (*): Column with transformation matrix. Will apply transformation matrix to content of pharmacophore/protein/ligand columns of the same row.

Input Ports

: Table containing pharmacophores in PHAR format and optionally proteins and/or ligands in PDB, SDF or Mol2 format

Output Ports

This node has no output ports

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Developers

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Installation

To use this node in KNIME, install the extension 3D-e-Chem KNIME nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.2

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

Plugin provider: Netherlands eScience Center

Plugin version: 2.0.3.v202311220951

On NodePit since: 2023-12-06

Last update: 2025-07-10

Tags: Deprecated

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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