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Site Selection

The Site Selection module allows users to select a binding pocket based on the positions of known ligands and extend the pocket size if necessary.


  • Different step results – Creates a new experiment where you can select a different result from this step.
  • Different starting parameters – Creates a new experiment where you can modify starting parameters before execution.

Uploading a Ligand​

In the Site Selection module menu, you can specify a reference ligand using one of two methods:


  1. Upload an .sdf file

  • Use the upload button to select a ligand file from your local storage.

Pay attention, that .sdf file should contain one reference ligand, which is located in appropriate coordinates regarding the protein structure.


  1. Use a reference ligand from the .pdb file

If you previously selected a reference ligand during the protein upload and project creation, you can enable the “Or use reference ligand from pdb” option.

Binding Site Visualization​

Once the binding site is generated:

  • It will be displayed as a semi-transparent pocket in the 3D visualization.
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  • A 2D representation of the reference ligand will also appear in the sidebar.
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Note: Similar to the Site Radar module, the generated binding site can be extended, but pocket characteristics are not calculated for sites derived from reference ligands.