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MD Pharmacophore Creator

LigandScout Extensions for the KNIME Workbench version 1.7.9 by InteLigand GmbH

The MD Pharmacophore Creator node processes a DCD/XTC trajectory and a macromolecule and gives a list of pharmacophores as result.

Options

Settings

Choose Active Site manually
If "Yes" is selected, you are able to choose the Active Site used in the process. Otherwise the biggest Active Site will be chosen.
Active Site selection
All Active Sites of the macromolecule are given, select the one you want to be used in the process.
Process all frames
The node processes all existing frames.
Process only ... frames (overall)
The node processes only a selected number of frames (in a constant interval). If the number is higher than the total number, the node prints only the available frames.
Process only every ... frames
The node processes only every X frame and skips the frames in between.
Index of first frame
Index of the frame with which the process should start.
(Default: 1)
Include Environment
Include the ligand environment in the pharmacophore output.
(Default: disabled)
Remove Water
Remove the water molecules before the pharmacophore generation.
(Default: disabled)
Remove Ions
Remove the metal ions before the pharmacophore generation.
(Default: disabled)

Input Ports

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Table containing one macromolecule-ligand complex
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Table containing one DCD/XTC trajectory

Output Ports

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Table containing pharmacophores for the specified frames

Views

Graph of Feature Frequencies
The view shows how often a (binned) frame contains a feature in the lapse. The bin-size can be adjusted.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install LigandScout Extensions for the KNIME Workbench from the following update site:

KNIME 4.3

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Developers

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