[Dock-fans] calculating binding sites volume overlap

[Ben Keshet]

Hi Dock-fans,

I want to calculate the degree of volume overlap of two ligands docked 
at close proximity (not at the same time). I thought of using sphgen to 
generate the positive (inside surface) representation of the ligands as 
a cluster of overlapping spheres. Then calculate the clusters volume 
(say V1 and V2), and calculate the overlapping volume of V1 with V2, 
which is the overlapping volume occupied by both ligands (separately, 
not at the same time).

Does anyone know a tool that can do something like that (Dock, Chimera 
or anything else)? Does anyone know if Mathematica is suitable for that? 
The analytical solution becomes complicated when the number of spheres 
increase, so I am trying to construct some numerical method to calculate 
the overlapping volume (but I am not a programmer so it's becoming time 
consuming). Any ideas are appreciated.

Thanks,
Ben Keshet
University of Maryland Baltimore County (UMBC)