ADL: Docking robustness

Stefano Forli forli at scripps.edu
Tue Dec 16 11:23:14 PST 2014


Hi Dariush,

there's no actual hard limit on the exhaustiveness value, so you should try experimenting 
with values that give you satisfactory results.
About the details you are interested in, try looking at the original paper on Vina [1] and 
the references mentioned there.

Best,

S


[1] http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/abstract

On 12/16/2014 08:11 AM, Dariush Mohammadyani wrote:
> 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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>>
> ________________________________________________
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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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