[Dock-fans] hi

Trent E. Balius tbalius at aol.com
Wed Jul 21 09:43:52 PDT 2010


 The Grid Score = VDW component+ ES component.
 

Trent 

 

-----Original Message-----
From: Pawan Gupta <pawanguptainfo at yahoo.co.in>
To: Trent E. Balius <tbalius at aol.com>
Sent: Wed, Jul 21, 2010 12:17 pm
Subject: Re: [Dock-fans] hi



thanks for ur answer
I already go through the manual which address u suggested me.
but want to know about how i correlate the these grid, vdw and electrostaic score to each other to define the pose or at a time we have to use only one score ??

thanks




From: Trent E. Balius <tbalius at aol.com>
To: pawanguptainfo at yahoo.co.in; dock-fans at mailman.docking.org
Sent: Wed, 21 July, 2010 6:15:27 AM
Subject: Re: [Dock-fans] hi


 
Hi Pawan,

See the following sections of the manual:

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GridEnergyScoring

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GridBasedScore

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Grid

The grid is used to speed up the energy calculation from O(n*m) where n is the number of atoms in the ligand and m is the number of atoms in the receptor to O(n*8) because you only look at the closed 8 grid points (there are 8 point on a cube).

I hope this helps,


 

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: Pawan Gupta <pawanguptainfo at yahoo.co.in>
To: dock6 FAQ <dock-fans at mailman.docking.org>
Sent: Wed, Jul 21, 2010 6:16 am
Subject: [Dock-fans] hi



what is the grid score in Dock6?
what is the vander waal score in Dock6?

How grid score can correlate with electrostatics and vander wal score?

i did not find detailed information about scoring functions in DOCk6 program


thanks in advance



 
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