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Article ID: 715 - Last Modified:

I'm having problems docking the Schrödinger fragment library to a protein-RNA complex.The job is encountering a very high rate of ligand rejection (>40% ). Is there anything I could do to rectify this?

During docking, the fragment centers explore the region of the inner box (10 Å by default). If the entire inner box is away from the receptor structure (perhaps because the native ligand, used to set the grid center, sticks out into solution), Glide may not be able to find poses of the small fragments that make good contacts with the receptor. Increasing the inner box size (under "Advanced Settings" on the Site tab) might help, as might moving the box center closer to the receptor surface.

Keywords: rejection rate, fragment docking, Glide

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