[Dock-fans] min anchor size -query

Sudipto Mukherjee sudmukh at yahoo.com
Wed Jul 11 20:55:21 PDT 2007


Mohamed,

The min_anchor_size is the minimum number of atoms used for the anchor. The value of 40 is artificially high. This makes dock use the largest rigid segment of the ligand as the anchor. If you want dock to consider more than one possible anchor, you can reduce this to a smaller size. '6' would likely pick benzene rings as the anchor. However, note that the full anchor and grow procedure is performed for each anchor. This might make docking run much slower, and yield a lot of similar poses. 
 
Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
Lab: 631-632-8519, Mobile: 631-220-5744


----- Original Message ----
From: "Abdul Hameed, MohamedDiwanMo" <mabdu3 at email.uky.edu>
To: "dock-fans at docking.org" <dock-fans at docking.org>
Sent: Wednesday, July 11, 2007 12:16:00 PM
Subject: [Dock-fans] min anchor size  -query




 
 

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Hello all,
 

  
 

I am trying target a small sub-pocket in a protein.  Will
it be useful to reduce the “min_anchor_size” parameter to 6 in that
case?
 

  
 

The default value is given as 40. I am also curious to
know whether changing this parameter will have any big impact on the results.
 

  
 

Your comments will be very helpful.
 

  
 

Thanks and Regards,
 

Mohamed Diwan
 

Graduate student,
 

University of Kentucky.
 




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