I have an alpha helix which loses its conformation after processing by LigPrep. Is there another way to prepare this type of ligand for docking?

The conformation generator in Glide includes a bias against compact ligand conformations (e.g., with internal H-bonds), since those are not observed as frequently as bioactive conformations. This may mean that Glide won't generate alpha-helical conformations, either.

An alternative is to generate alpha-helical conformations externally (e.g., with MacroModel, using restraints on the backbone) and then dock those conformations rigidly.

Keywords: alpha-helical conformations

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