I have a congeneric series of compounds I would like to dock with Glide, but I want the common scaffold of the ligand series to always dock into the same position - I want it to have the same scaffold position as the lead compound does in my crystal structure. Can I do this with Glide?

When you're setting up a Glide job, in the Core tab, choose "Restrict docking to reference position". Then, click on your lead compound in the Workspace to define the core-containing molecule. Go to the Maestro Workspace and use atom-selection from the toolbar to select only the core atoms. Then go back to the Glide panel and choose to define the core atoms by "SMARTS pattern" and click "Get from selection".

You can decide whether you want to "skip ligands that do not match core pattern" or not. If all your ligands contain the relevant SMARTS atoms then it won't matter what you pick for this option.

Keywords: Glide, Maestro

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