Calculate volume of the binding site and molecules: Difference between revisions

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Written by Trent Balius, Dec. 2016.  
Written by Trent Balius, Dec. 2016.  


==The the volume calculation works.==
==how the volume calculation works.==


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


   Vs = Ns/Ng * Vb
   Vs = Ns/Ng * Vb
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==Calculating the volume of a binding site.==
==Calculating the volume of a binding site.==


You can run blastermaster.py which is distrubuted with DOCK3.7 and then use the lowdielectric.sph to define the pocket.
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:
Alternatively, you can do the following:


(1) run dms (or you can also generated the molecular surface with Chimera) to generate a molecular surface.
* run dms (or you can also generated the molecular surface with Chimera) to generate a molecular surface.
   
   
(2) Use sphgen (destrbuted 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. Copy the sphere file. Using a text editor (vim) remove all clusters except the one of interest.   
* 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:
* Calculate the volume using the following script:
[http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]
[http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]


Revision as of 21:42, 4 December 2016

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.

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