[Dock-fans] Dealing with very large receptors

Trent E. Balius tbalius at aol.com
Thu Jan 13 16:15:18 PST 2011


 Hi francesco, 
  
I think that option (2) is reasonable.
  
One can use a 0.4 resolution grid without sacrificing much in accuracy.
  
I would not recommend using a grid with 0.6 resolution.  
  
Option (4) is better in my opinion. 
  
How are you partitioning your protein?
  
The program grid will read in a protein and a box and generate a grid. 
  
Grid points are calculated only within the box.  All of the protein is considered at every grid point; 
i.e. the program grid calculates the potential energy felt at the grid point exerted by the protein.
  
See the manual:
  
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Grid
  
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GridEnergyScoring  
  
You can think of the grid as a potential energy field.  
  
in order to create grids all over your protein surface one should read in the same protein but use a different box.  
  
My advice is to focus in on likely binding pockets and generate 0.3 grids about them.
  
Visualize the spheres to help select deep cavities and areas of curvature
  
Good luck,
 

Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Francesco Pietra <chiendarret at gmail.com>
To: dock-fans <dock-fans at docking.org>
Sent: Thu, Jan 13, 2011 4:24 pm
Subject: [Dock-fans] Dealing with very large receptors


Hello:

When forced to carry out blind docking in the absence of any ad hoc

information, while the protein is too large to work with a grid (at

least at 0.3 resolution), which chances are left to proceed soundly?



(1) Abandon the case, no hope.



(2) Use a larger grid resolution. How much large could it be?



(3) Docking without using a grid.



(3) Do at grid 0.3 resolution but select portions of the protein, one

each time. This one I tried. No reliable results.



Thanks for comments



francesco pietra

_______________________________________________

Dock-fans mailing list

Dock-fans at mailman.docking.org

http://mailman.docking.org/mailman/listinfo/dock-fans


 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20110113/6a39f90e/attachment.html 


More information about the Dock-fans mailing list