Article ID: 707 - Last Modified: September 20, 2012
What's the best way to filter out poses with bad torsions?
The ligand strain calculation might remove such poses, or you could remove poses with high Einternal. Neither of these are ideal solutions, because they operate on the ligand conformation as a whole, in which there are a variety of compensating interactions. Also, because Glide uses a rigid receptor structure, filtering out poses with 'bad' torsions could result in false negatives.
Post-processing using MacroModel (Embrace) or Prime (MM-GBSA) could generate ligand poses with improved torsions, or discriminate between poses with good torsions and ones with bad torsions. Another alternative might be to relax the receptor in an Induced Fit Docking calculation if there are only a few poses under consideration.
If you know beforehand which torsions are problematic, you can use torsional constraints when docking the ligands to eliminate poses with bad torsions. These constraints can be set up in the Torsional Constraints tab of the Ligand Docking panel.
Keywords: Glide, bad torsions, filter poses
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