ADL: Which conformation is the "true conformation"?

mcmartin at mcmartin at
Thu Apr 23 08:30:55 PDT 2009


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?

Watching the Vina tutorial video was very clarifying, since Oleg Trott
showed the theory behind docking programs and the relationship between
conformations, loss of entropy and energy values, where he clearly picks
the conformation that the program assumes is the one correct. Do you know
how to make a graphic representation like that?


> In my opinion, the docking results must be test in "real" function
> experiment to determine which one is the ture. dock result just can be and
> suggestion not the final results.
> ÔÚ2009-04-23£¬mcmartin at дµÀ£º
>>When analyzing the results, say in blind docking, do you guys just assume
>>that the conformation of lowest energy of all runs is the conformation
>>more likely to be the native conformation (true conformation)? I'm asking
>>because I have absolutely no idea how to decide which conformation is
>> true
>>based on the binding energy coupled to the RMS values. So I just look at
>>the screening summary and pick the lowest energy and assume this could be
>>the conformation more likely to come up in an NMR/X-ray experiment.
>>So I watched the Vina tutorial video and Oleg shows a graph that depicts
>>the free energies of binding in relation to the hypervolume defined by
>> the
>>ligand's state variables: translations, rotations, torsions. Does anyone
>>know how to make such a graph?
>>With kind regards
>>Marcus Martinez
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