Article ID: 665 - Last Modified: October 1, 2013
Is it possible to keep a receptor side chain flexible during Glide docking? If so, how do I do this?
Glide is a rigid-receptor docking program. However, during Grid Generation, you can request that specific active site hydroxyl or thiol groups be considered rotatable, so they will be sampled during docking. This feature was introduced in Glide 5.5 (Suite 2009).
If you want to investigate receptor conformation changes that occur when binding ligands, we recommend our Induced Fit Docking (IFD) workflow, which uses both Glide (for docking) and Prime (for side-chain optimization).
If there are induced-fit effects upon binding ligands, you could try an ensemble docking approach with our Virtual Screening Workflow, by which you could dock ligands to multiple receptor conformations (e.g., alternative crystal structures, or models generated by IFD).
Keywords: flexible receptor side chain, IFD, Glide, docking
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