Knowledge Base

I want to align a set of ligand-like molecules that are not conformers. How do I do this?

If you want to align the molecules by their shape, you can use Shape Screening (Tasks → Shape Screening in Maestro). You will need to use one of these molecules (or some other target molecule) as the query, and align all the other molecules to this molecule. In the Shape Screening panel:

  1. Set up the source of the query and the structures to align.
  2. Select Atom types for Volume scoring.
  3. Choose None from the Atom types for volume scoring option menu.
  4. Deselect Generate conformers.
  5. Click Run.

If you want to weight the alignment towards aligning certain features or atom types, you can choose other atom types from the option menu, or select Pharmacophore types.

This procedure performs a rigid alignment of the existing molecules. If instead you want to allow for conformational flexibility during the alignment, you should leave the Generate conformers option on, and then for each input structure, the structure that is returned will be the best match of any of the generated conformers to the shape of the query structure.

For a small number of molecules you can perform a flexible alignment on structures in the Project Table, with Tools → Flexible Ligand Alignment.

To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.

Back To Top