[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.



> Be happy we are dock FANS!
> Best regards!
> Gustavo HMF Souza
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans

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