ADL: Docking robustness

Dariush Mohammadyani d.mohammadyani at gmail.com
Tue Dec 9 14:50:18 PST 2014


Thank you Amr!
The issue is lack of robustness. If you use same ligand and receptor and
run several dockings using different seed, your results would be different
in each run.
Then, how you can find out the main binding pose or study binding energies?
Specifically, in a case of comparing different ligands vs. the same
receptor.


Regards,
Dariush

On Tue, Dec 9, 2014 at 5:01 PM, Amr AL-HOSSARY <amr_alhossary at hotmail.com>
wrote:
>
> Vina is supposed to do a stochastic search using both Monte Carlo and BFGS
> methods.
> The seed is used to control the randomness by giving a fixed start point if
> you need.
>
> I don't see any "issue" there to mitigate.
>
> Amr
>
>
> -----Original Message-----
> From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu]
> On
> Behalf Of Dariush Mohammadyani
> Sent: Tuesday, December 09, 2014 5:28 AM
> To: autodock at scripps.edu
> Subject: ADL: Docking robustness
>
> Hello All,
>
> I am wondering to know why changing the seed (using -seed option) results
> in
> significantly different results.
> For instance, in one docking most of 9 models may represent a binding pose,
> which can be different from the results of another docking using different
> random seed number.
>
> How can I mitigate this issue?
>
> Thank you for answering!
>
> Regards,
> Dariush
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