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Article ID: 355 - Last Modified:

I want to see only the top pose for each ligand from a Glide docking run, and step through these poses by ligand. How do I do this?

By default, the ligands are ordered by GlideScore, so when you step through the poses, you might have several poses from a given ligand before you come to poses from another ligand. This can happen if you used Epik to expand tautomeric or ionization states in your input ligands, or generated conformers outside Glide (e.g. with ConfGen or MacroModel), or you chose to write out more than one pose per ligand.

To select a single pose for each ligand, the ligand must be able to be identified by the value of a particular property. Usually this is the title, which we will assume is the case here, but you could use any property that identifies the ligand, such as a SMILES string property.

Maestro has two ways of selecting the top pose for each ligand, making use of the values of a property. The first is done in the Project Table itself, as follows:

  1. Select the entry group containing the ligands.
  2. Right-click on the property column (Title, for example) and choose Deselect Duplicate Values.

The first ligand for each value of the property is selected, and the entries for all other occurrences of the property are deselected. This method relies on the ligands being sorted by the desired property, such as the GlideScore. If the ligands are not sorted by the desired property, you can use the second method, which selects the ligands after sorting.

  1. Select the entry group containing the ligands.
  2. Click the Sort button on the Project Table toolbar, which opens the Sort Project Table panel.
  3. Choose the property to sort by from the list on the left, e.g. "docking score" or "glide gscore"
  4. Make sure Sort entries is selected.
  5. Click the arrow button under Sort entries, to add the property to the sort list, and ensure that the sort direction is correct. (If not, click the Direction cell to change it).
  6. On the lower right, select "After sorting, select top"
  7. Select Unique entries in each group, by property
  8. Click the button with the table icon (to the right of the text box) and choose the property that defines the ligand (e.g. Title)
  9. Click Sort Selected.

The entries in the group should now be sorted and the top entry for each ligand should be selected.

You can now step through the entries with the left and right arrow keys, as you do in Pose Viewer mode.

For releases earlier than 2015-2, these two features are not available, but you can select the top pose for each ligand with the following procedure:

  1. Select all ligands and poses in the Project Table.
  2. Choose Entry → Group by Entry Property and group the entries by Title. If you have ligands from different tautomers or ionization states but with the same title, you might want to group by "glide lignum" instead.
  3. With all poses now grouped and still selected, click the Sort button on the Project Table toolbar and sort by "glide gscore" (or "docking score"), in ascending order.
  4. Choose Group → Collapse → Selected in the Project Table

You can now step through the top poses for each ligand by stepping through the resulting groups with Shift+Right Arrow. If you find a top pose for which you also want to see other poses, you can then use just Right Arrow (which steps through entries in the group). To display the top pose for the next ligand, use Shift+Right Arrow again (which steps through groups).

Keywords: project table

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