ADL: grid box help

Keti Bardhi keti.bardhi at hotmail.com
Thu Dec 18 06:50:04 PST 2014


Based on your experience  how do you draw conclusions  on the results. I am docking one protein with several ligands and trying to find one with good affinity. How can I download this program that you attached me ?Thank you..

> Date: Wed, 17 Dec 2014 22:05:49 +0000
> From: devl.development at gmail.com
> To: autodock at scripps.edu
> Subject: Re: ADL: grid box help
> 
> Hi Keti
> 
> I'm not sure if this helps, but I have a tool that helps generate bounding
> boxes based in amino acid positions in Angstroms.
> 
> https://github.com/devldevelopment/dockingbox
> 
> Normally I define boxes around amino acids of interest and add extra space
> to the bounding box to allow ligand flexibility. Vina is a
> stochastic/statistical method so it's likely that even with the same box
> you will get different affinities. By no means am I an expert these are
> just my thoughts and experiences. Please let me know if you want help with
> the tool or what your particular use case is.
> 
> Cheers
> Dev
> 
> 
> 
> On Wed, Dec 17, 2014 at 8:35 PM, Keti Bardhi <keti.bardhi at hotmail.com>
> wrote:
> >
> > Hello, I am new to Autodock Vina and I am having a problem in defining
> > the grid box coordinates.  Does the binding affinity change in base of the
> > grid box coordinates. How precise should they be ? I have tried different
> > ways to calculate the grid box and I get different binding affinities.
> >
> > Thank you.
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