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Article ID: 251 - Last Modified:

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

The best option is to use 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 (VDW) for the surface map in the "Manage Surfaces" panel.

There is no user input for the site volume, so you cannot control how far into the solvent the site extends. However, you can visualize the volume points used for the volume calculation by runnning SiteMap from the command line with the -keepvolpts option, and then importing the resulting PDB file.

There is a script available in the installation that runs a SiteMap calculation on a series of structures or on each frame of a Desmond trajectory,trajectory_binding_site_volumes.py.

Keywords: active site, binding site, volume, Maestro

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