Is there a way to exclude sites from consideration in the search for common pharmacophores?
Yes, you can do this in Suite 2010 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
