ADL: Docking robustness

Dariush Mohammadyani d.mohammadyani at gmail.com
Tue Dec 16 08:11:49 PST 2014


Thank you Stefano!

Do you know what is the range of exhaustiveness? If there is no concern for
processing time, can I set it to maximum value?
Actually I changed it to 14, and I got higher robustness, in term of energy
and pose.

One more request:
I would highly appreciate if you offer any practical documents with some
algorithmic details of docking (more detailed than manual).

Regards,
Dariush

On Tue, Dec 9, 2014 at 8:23 PM, Stefano Forli <forli at scripps.edu> wrote:
>
> Hi Dariush,
>
> you may want to take a look at this page [1] for a general discussion
> about variations among docking results.
> As a rule-of-thumb, inconsistencies across docking run imply lack of
> convergence, therefore very likely the search is not accurate enough to
> sample the energy landscape of your problem.
>
> To overcome this issue you can either reduce the complexity of the search
> (e.g., reduce docking box dimensions or split it into multiple boxes;
> rigidify parts of the ligand) or increase the search length (e.g., increase
> exhaustiveness).
>
> About random seeds, they are set automatically by the docking programs,
> and the only reason to manually set one would be to exactly reproduce a
> particular docking job.
>
> Hope this helps,
>
> S
>
>
>
> [1] http://autodock.scripps.edu/faqs-help/faq/why-do-the-
> results-differ-when-multiple-dockings-are-done-with-the-
> same-input?searchterm=calculation
>
>
> On 12/09/2014 02:50 PM, Dariush Mohammadyani wrote:
>
>> 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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>>
> --
>  Stefano Forli, PhD
>
>  Staff Scientist
>  Molecular Graphics Laboratory
>  Dept. of Integrative Structural
>   and Computational Biology, MB-112F
>  The Scripps Research Institute
>  10550  North Torrey Pines Road
>  La Jolla,  CA 92037-1000,  USA.
>
>     tel: +1 (858)784-2055
>     fax: +1 (858)784-2860
>     email: forli at scripps.edu
>     http://www.scripps.edu/~forli/
>
> ________________________________________________
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