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Article ID: 927 - Last Modified:

I would like to use Glide to dock to an RNA molecule that is rather large. How can I generate a grid for my target?

From Suite 2010 on, Glide supports up to 90,000 atoms in the receptor. If the RNA target is too large, you might have to truncate it for use with Glide. You can do this as follows:

  1. Import the structure into Maestro.
  2. Click the Atom selection toolbar button, and select the native ligand, if it exists, or residues in the binding site.
  3. Choose Select from the Atom Selection toolbar button, to open the Atom Selection dialog box.
  4. Click the Selection button.
  5. Click Proximity, to open the Proximity dialog box.
  6. Under Proximity, select Within and Angstroms, and enter a distance from the active site to truncate the structure (e.g. 25).
  7. Under Fill, select Residues.
  8. Click OK in the Proximity dialog box, and again in the Atom Selection dialog box.
  9. Choose Select from the Delete toolbar button, to open the Atom Selection dialog box.
  10. In the ASL text box, type the following expression:

    not (atom.selected or withinbonds 1 (atom.selected and atom.ele P))

    The purpose of this expression is to complete the phosphates, which are cut between the P and the O, and then invert to delete the atoms that aren't selected.
  11. Click OK. The RNA structure should now be truncated, and all phosphates on the boundary should be complete.
  12. Run the Protein Preparation Wizard on the structure, and proceed to grid generation as usual.

Keywords: RNA, Glide, docking

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