MD Pharmacophore Creator

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



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

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

Output Ports

Table containing pharmacophores for the specified frames


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


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