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Article ID: 1347 - Last Modified: April 30, 2012

Is there a way to exclude sites from consideration in the search for common pharmacophores?

From Suite 2011, you can exclude sites in the Create Sites step, by including ligands in the Workspace, and selecting the sites in the Excluded features list.

In Suite 2010 you can do this with the following procedure.

1. Complete the Create Sites step of the Develop Pharmacophore Model workflow, using a named project, here called project.prj.

2. In the Ligands table of the Create Sites step, select each active that contains sites to be excluded.

3. Right-click and choose Export Conformers to Project Table.

4. In the Project Table, select the first conformer of each exported active.

5. For each selection in step 4, use the Manage Hypotheses panel to create a hypothesis containing only the sites to be excluded for the corresponding ligand.

6. Select all rows in the Hypotheses table, and export the hypotheses to an empty directory, here called hypoDir.

7. Run the Phase program exclude_sites to mark the applicable sites in the project as inaccessible. A sample command is as follows:

$SCHRODINGER/run -FROM phase exclude_sites project.prj run hypoDir -exclude

Here run is the Phase run number (1, 2, etc.). Unless you\'ve created multiple runs in the project, it should be 1. You should see a series of messages like:

Excluding sites in project.prj/.mmproj-admin/phase_confsets/phase_confset.n/1_v1.0

followed by

exclude_sites successfully completed

You can now proceed to the Find Common Pharmacophores step. You should observe that the excluded sites do not appear in any common pharmacophore.

If you wish to reverse the whole exclusion process and go back to the original sites, you can run the following command:

$SCHRODINGER/run -FROM phase exclude_sites project.prj run hypoDir -restore

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