Article ID: 665 - Last Modified: May 27, 2014
Is it possible to keep a receptor side chain flexible during Glide docking? If so, how do I do this?
Glide keeps the receptor rigid during docking, while allowing conformational flexibility for the ligands. However, during grid generation, you can choose to allow specific active site hydroxyl or thiol groups ("rotatable groups") to sample different rotamer configurations 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 also 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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