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Article ID: 202 - Last Modified:

I used SiteMap to find the binding pocket in my structure and now I want to do docking. Is it possible to use the SiteMap definition of the binding site as input to Glide?

You can generate a grid from a SiteMap binding site as follows:

  1. Include both the receptor and the desired SiteMap binding site entry in the Workspace.
  2. Open the Receptor Grid Generation panel (Applications → Glide → Receptor Grid Generation).
  3. Choose Entry from the Pick to identify ligand option menu in the Receptor tab.
  4. Pick one of the site points (the white spheres).
  5. Continue with the rest of the grid generation setup, and run the job.

The set of site points is likely to produce a default grid box size that is too large if you set the box size by the size of the ligand. You can use the Dock ligands with length <= slider to make the box size more reasonable.

If the site is not well defined or the site points extend over a broad region, the center of the site points might not be the best place for the grid box center. In that case, you can define the grid box center in terms of selected residues bordering the site, with the Centroid of selected residues option.

Keywords: SiteMap, site points, Glide, grids, Maestro

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