ADL: Which conformation is the "true conformation"?

许文 xuwenpku at
Thu Apr 23 06:30:40 PDT 2009

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.

在2009-04-23,mcmartin at 写道:
>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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