View and Edit Pharmacophore Files

The SilcsBio GUI provides a convenient platform to view and edit existing pharmacophore files. The pharmacophore model viewing and editing platform can be accessed by choosing View/Edit Pharmacophore File from the Home page of the Small Molecule Suite.


Using this tool, users can view the pharmacophore feature in the context of the target protein and the corresponding FragMaps, measure distances between pharmacophore features, select or deselect pharamacophore features in the pharmacophore model, adjust the feature radii, and save the modified pharmacophore model into a new pharmacophore file.

Instructions for viewing and editing exisitng pharmacophore files are provided below.

  1. Enter the pharmacophore file:

    Provide the pharmacophore file to be viewed or modified. To guide the selection of pharmacophore features to modify, the user may also provide the struture of the target protein and the corresponding FragMaps. If the target protein and FragMaps are loaded, ensure that the pharmacophore file was created using the same input protein and FragMaps. Click “Show” to proceed.

  2. Edit the pharmacophore feature selection:

    After clicking “Show”, the GUI will display the pharmacophore features. The “Pharmacophore” tab will list all the pharmacophore features from the input pharmacophore file. From this window, the user can measure the distance between features, select or deselect features, and increase or decrease feature radii.

  3. Save the new pharmacophore model:

    After finalizing pharmacophore feature selection and adjustment, the new pharmacophore model can be saved by clicking either of the “Save Feature” buttons. The pharmacophore model can be saved in .ph4 format compatible with either Pharmer or MOE.



The exclusion pharmacophore features are NOT supported by Pharmer.