Calculate volume of the binding site and molecules

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Written by Trent Balius, Dec. 2016.

how the volume calculation works.

  • First, Lay a grid over the spheres.
  • Count the number or points contained in the spheres (Ns).
  • Count the number of points in the grid box (Ng).
  • Calculate the volume of the grid box (Vb).
 Vs = Ns/Ng * Vb

Calculating the volume of a binding site.

You can run which is distributed with DOCK3.7 and then use the lowdielectric.sph to define the pocket.

Alternatively, you can do the following:

  • run dms (or you can also generated the molecular surface with Chimera) to generate a molecular surface.
  • Use the sphgen program(distributed with all versions of DOCK) to flood the surface of the protein with spheres, which are then cluster by distance.
  • Select the cluster that defines the binding site of interest by visualization in Chimera.
  • Copy the sphere file. Using a text editor (vim) remove all clusters except the one of interest.
  • Calculate the volume using the following script:

Calculating the volume of a small molecule.

Convert ligands to spheres.