Pharmacophores Viewer

This Node Is Deprecated — This node is kept for backwards-compatibility, but the usage in new workflows is no longer recommended. The documentation below might contain more information.

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

Icon
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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Links

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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:

v4.6

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

Plugin provider: Netherlands eScience Center
Plugin version: 2.0.2.v201911071546
On NodePit since: 2022-06-11
Last update: 2022-12-06
Tags: Deprecated
KNIME versions: From v3.6 to v4.6