[Dock-fans] Multiple ligands

Gustavo HMF Souza desouz at fcm.unicamp.br
Tue Oct 3 21:02:35 PDT 2006


Dear Kim,

 

Thank you for your kindly reply. I`ll try this that you mentioned above.

 

Best wishes!

Gustavo.

 

From: Kim Branson [mailto:kim.branson at gmail.com] 
Sent: Wednesday, October 04, 2006 12:45 AM
To: koraxgh at gmail.com
Cc: dock-fans at docking.org
Subject: Re: [Dock-fans] Multiple ligands

 

 

On Oct 3, 2006, at 8:27 PM, Gustavo HMF Souza wrote:

 

 

Hi Gustavo, 



 

After running dock many times with one ligand and one receptor, I want to
know if is possible to construct a ligand database (with 50 different
ligands for example) and run all with the same receptor. So, 





this is certainly possible. As you state the best thing is to charge and
protonate your ligands.  then cat them together into a single mol2 file.

 

You can set up a single dock.in file by editing an existing one, and then
running dock6 -i dock.in -o dock.out -v2  . The dock.out will contain the
results from dock. 

 

To rank your database, limit_max_ligands  = no ( you want to  read them all
in)  and you want to set rank_ligands to yes.  set max_ranked_ligands to be
the size of the list you are interested it, i.e top 100 or 500 etc.

 

from the dock6 manual:

 

# rank_ligands [no] (yes, no):

#Flag to enable a ligand top-score list. These ligands will be written to

#outfile_ranked.mol2, and outfile_scored.mol2 will be empty by default

 

    * max_ranked_ligands [500] (int):

      #The number of ligands to be stored in the top score list

    * scored_conformer_output_override [no] (yes, no):

 





 

Third: After all of this, how can I calculate a Ki constant for each one of
them? (This, assuming that all calculations is o.k. and I have a previous
pre-computed receptor grid.nrg ready to ./dock).





This is hard. But since you have 50 ligands, you might consider the
application of a more complicated scoring method. You could rescore all your
ligands with Amber score, which should correlate roughly with the binding
affinity, and hence the Ki.  If you have  a few known ligands for your
system you can use that too see how accurate your prediction is.

 

cheers

 

Kim 

 





 

Be happy we are dock FANS!

 

Best regards!

Gustavo HMF Souza

UNICAMP.

 

 

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