View source for 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: [http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]


== Calculating the volume of a small molecule. ==

Convert ligands to spheres.