Calculate volume of the binding site and molecules

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 blastermaster.py 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:

volume_cal_sph.py

Calculating the volume of a small molecule.

Convert ligands to spheres.