Article ID: 729 - Last Modified: August 19, 2014
I want to dock a molecule with a pharmacophore feature at an active site of an enzyme so that I can see its interaction with the donor and acceptor feature. How can I do this?
Glide supports several types of docking constraints (H-bond, metal, positional/NOE, torsional, core). You should be able to use some of these constraints types to select ligand poses similar to your pharmacophore. For all constraint types except core constraints and torsional constraints, specification of the receptor atoms or active site regions involved in the constraint must be provided during the Grid Generation setup.
During the Ligand Docking setup, the ligand features able to satisfy the constraint (custom SMARTS patterns, or default features like "H-bond donor") must be specified. Core constraints are specified via a reference molecule during Ligand Docking setup.
When the job finishes, you can visualize the results by using Entry → View Poses in the Project Table panel.
Keywords: pharmacophore, docking, constraints, Glide
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