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Article ID: 467 - Last Modified:

I want to calculate the surface area of a protein binding site, defined as any residue 6 Å from the ligand, and also the volume of the binding site. How do I do this?

For the surface area, there are several options.

  • Use the Create Binding Site Surfaces panel, which you can open with Workspace → Surface → Create Binding Site Surfaces. You can set the distance from the ligand in this panel. The surface area of each surface is reported in Å2 in the Manage Surfaces panel.
  • Use the Binding Surface Area Analysis panel, which you can open with Scripts → Project Table → Binding Surface Area Analysis.
  • Use the Molecular Surface panel, which you open with Workspace → Surface → Molecular Surface. Use the following ASL expression for the surface:
    not (mol.entry 2) and fillres within 6 (mol.entry 2)
    assuming your ligand is molecule #2 in the complex structure. Make sure that "Surface Context" is set to "Molecule"; also if your ligand is covalently bound or has zero-order bonds to the receptor (and thus not considered a separate molecule) you might want to break the bonds first using Delete → Bonds or Delete → Zero-Order Bonds from the Delete toolbar button. The area of the surface (Connolly) is reported in the Manage Surfaces panel, in Å2.
  • The installation has scripts for calculating the solvent-accessible surface area of a ligand in a receptor (, and the change in surface area on ligand binding ( which you can run with $SCHRODINGER/run script.

Probably the best option for the volume is to use Applications → SiteMap. You can pick the ligand to specify which site to consider and how far from the ligand to extend the buffer region. The SiteMap job reports the site volume in the Project Table and also reports the surface area for the surface map in the "Manage Surfaces" panel.

Keywords: measurement

Related Articles:

#251: How do I calculate the binding site volume and report the result in Å3 in Maestro?

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