View source for Calculate volume of the binding site and molecules


Written by Trent Balius, Dec. 2016. 

The script to calculate volume is available here: [http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]

 syntax: python volume_cal_sph.py input.sph spacing output_prefix

 example: python volume_cal_sph.py binding_site.sph 0.5 binding_site 

download using curl as follows:
 curl http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py > volume_cal_sph.py
 curl http://docking.org/~tbalius/code/for_dock_3.7/mol2.py > mol2.py
 curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
 curl http://docking.org/~tbalius/code/for_dock_3.7/mol2toSPH_radius.py > mol2toSPH_radius.py


==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

*This method also produces dx files, so you can visualize (using chimera or VMD)the volume as grids.

==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 using the following script: [http://docking.org/~tbalius/code/for_dock_3.7/mol2toSPH_radius.py mol2toSPH_radius.py]

Say, you would like to calculate how much two docking poses overlap in volume: 

Convert the mol2 files to sph files: 
 
 python ~/zzz.scripts/mol2toSPH_radius.py molone.mol2 molone.sph
 python ~/zzz.scripts/mol2toSPH_radius.py moltwo.mol2 moltwo.sph

Create a combined sphere file:

 cat molone.sph > bothmol.sph
 sed -e 's/cluster     1 /cluster     2 /g' moltwo.sph | grep -v DOCK >> bothmol.sph

 >> python ~/zzz.scripts/volume_cal_sph.py molone.sph 0.5 molone
 input file =  molone.sph
 scale = 0.5
 outputprefix = molone
 max corner =  51.964 41.34 37.041
 min corner =  39.322 31.367 28.854
 0.5 26 20 17 0.5 0.5 0.5 [39.321999999999996, 31.366999999999997, 28.853999999999999]
 molN= 1502   boxN= 8840   boxV= 1105.0
 molV= 187.75

 >> python ~/zzz.scripts/volume_cal_sph.py moltwo.sph 0.5 moltwo
 input file =  moltwo.sph
 scale = 0.5
 outputprefix = moltwo
 max corner =  49.176 38.767 36.529
 min corner =  39.059 31.2 27.753
 0.5 21 16 18 0.5 0.5 0.5 [39.058999999999997, 31.199999999999996, 27.753]
 molN= 1257   boxN= 6048   boxV= 756.0
 molV= 157.125

 >> python ~/zzz.scripts/volume_cal_sph.py bothmol.sph 0.5 bothmol
 input file =  bothmol.sph
 scale = 0.5
 outputprefix = bothmol
 max corner =  51.964 41.34 37.041
 min corner =  39.059 31.2 27.753
 0.5 26 21 19 0.5 0.5 0.5 [39.058999999999997, 31.199999999999996, 27.753]
 molN= 1868   boxN= 10374   boxV= 1296.75
 molV= 233.5

The overlap region may be calculated as follows: 

 157.125 + 187.75 - 233.5 = 111.375