ADL: Which conformation is the "true conformation"?

mcmartin at student.matnat.uio.no mcmartin at student.matnat.uio.no
Fri Apr 24 13:00:04 PDT 2009


Thanks again Mark! This is exactly what I needed :)

> On Thursday 23 April 2009 10:30:55 am mcmartin at student.matnat.uio.no
> wrote:
>> Hi,
>>
>> I'm fully aware of the limitations of docking software and that it
>> should
>> only be used as some kind of guidance prior to in vitro experiments.
>> Having said that, I'm trying to understand the results for several
>> compounds in which each docking gave me an .dlg output file with 200
>> different conformations ranged by binding energy values and dissociation
>> constants. So my question is, do you guys just pick the conformation of
>> lowest energy and work further upon that? Or do you look upon the
>> clusterings and see the number of conformations per energy value? Or the
>> RMSD values?
>>
> I was just looking at a recent paper that might address your concerns:
>
> http://www.ncbi.nlm.nih.gov/pubmed/18351616
>
> http://www3.interscience.wiley.com/cgi-bin/fulltext/117943606/HTMLSTART
>
> One interesting observation from their test cases was that random
> selection of
> a conformation (from the set of LGA solutions produced by autodock) was,
> on
> average, more successful (in terms of RMSD relative to the experimental
> conformation) than picking the lowest energy conformation. Lowest-energy
> was
> correct for 3/22 complexes and random had an expectation of 12.35/22
> cases.
> Now, they were looking at weakly interacting complexes so the really poor
> performance of the scoring function here is probably not generally
> applicable.
>
> OTOH, using the scoring function but applying a correction factor based on
> the
> cluster populations was successful in 16/22 cases. This is probably your
> best
> bet if you don't want to do consensus scoring.
>
> Regards,
>
> Mark
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