[Dock-fans] Multiple ligands

Kim Branson kim.branson at gmail.com
Tue Oct 3 20:44:38 PDT 2006


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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> Dock-fans at docking.org
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