Article ID: 663 - Last Modified: December 4, 2010
I want to dock a peptide for which the position of one residue is known from the X-ray structure. Is there a way that I can keep this residue fixed and dock the rest?
You could try using a single core constraint. Core constraints are defined during the docking setup (on the Core tab). You'll need to have a pre-positioned reference ligand in the Workspace (from a crystal structure, or placed by hand). Since you only want one residue to be the core, select that residue in the Workspace and use the "Get From Selection" option to generate the core SMARTS pattern. When you dock your peptide, Glide will try to keep the part of the peptide that matches the SMARTS pattern in the specified reference location.
Keywords: core constraints, Glide, peptide
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