[Dock-fans] reg free energy calculation

Trent E. Balius tbalius at aol.com
Fri Mar 22 13:03:02 PDT 2013


Hi Vishwambhar 

Scoring functions in DOCK (many of which approximate the binding free energy) have different levels of accuracy.  

See the following for a discussion of DOCK Score: 

http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#whatisascore



 You might consider using the amber score for your calculation:  

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

Here is a docking tutorial:
http://ringo.ams.sunysb.edu/index.php/2013_DOCK_tutorial_with_Orotodine_Monophosphate_Decarboxylase

Here is a Amber Score tutorial:
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm

 
Depending on the accuracy that you need, you may need to use an alternative program such as AMBER. 

I hope this helps,

Trent


======================================
Trent E. Balius, PhD
Shoichet Lab – Dept. of Pharm Chem,
University of California, San Francisco
           1700 4th Street
           Box 2550
           San Francisco, CA 94158     
Office: Byers Hall, Rm 509
URL: http://docking.org/~tbalius
======================================

 

 

-----Original Message-----
From: Vishwambhar Bhandare <vishwayogi at gmail.com>
To: dock-fans <dock-fans at docking.org>
Sent: Sat, Mar 9, 2013 6:52 am
Subject: [Dock-fans] reg free energy calculation



Dear all, 

I Have to do free energy calulations using dock6.5 

Is there any tutorial or guide available for doing this???



Thanks and Regards, 
--------------------------
Vishwambhar 
Centre for Bioinformatics 
Pondicherry University
Pondicherry
--------------------------

Note: Strictly confidential to Vishwayogi




 
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