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Article ID: 253 - Last Modified:

Is it possible to treat tautomeric forms of a ligand as interchangeable when developing a pharmacophore model?

Yes, you can treat tautomers as interchangeable. There are two ways of doing so:

  • By using the Develop Common Pharmacophore Hypotheses panel in Maestro, and defining ligand groups.
  • By running the Develop Common Pharmacophore Hypotheses workflow from the command line. A detailed tutorial that takes you through the command-line pharmacophore generation is in:
    $SCHRODINGER/phase-vversion/tutorial/pharm_tutorial.pdf
    In particular, in Section 1.5 it is shown that the tautomers and their conformations can be assigned to the same LIGAND_GROUP, and they will then be treated as interchangeable when perceiving common pharmacophores.

Keywords: Phase, tautomers, common pharmacophore

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