ADL: Which conformation is the "true conformation"?

mcmartin at student.matnat.uio.no mcmartin at student.matnat.uio.no
Thu Apr 23 01:40:38 PDT 2009


Hi,

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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