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I would like to do ensemble docking for some proteins in which residues in the binding site adopt different dihedral angles. How do I do this?

The Induced Fit Docking (IFD) protocol, which uses Glide and Prime to allow the receptor to adjust to the ligand, is our recommended method for generating alternative receptor conformations for use in ensemble docking. We suggest running IFD on a few known active compounds, and then taking the top IFD structure from each active for the ensemble.

For the ensemble docking itself, we recommend our Virtual Screening Workflow (VSW, on the Workflows menu in Maestro). This workflow facilitates ensemble docking with multiple receptor conformations (and optional GlideScore offsets), and also multi-stage screening of large databases.

Both of these workflows have user manuals in our documentation set. For more information on IFD, see the following publication:

Sherman, W.; Day, T.; Jacobson, M. P.; Friesner, R. A.; Farid, R.,"Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects", J. Med. Chem., 2006, 49, 534 -553

If you are interested only in the orientation of hydroxyl groups in the binding site, you can use the Rotatable Groups feature in Glide grid generation to allow these groups to adopt different conformations during docking. You can then use a single grid to obtain results for multiple orientations of these groups.

Keywords: ensemble docking, IFD, Glide

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