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Display of results
We used jmol to create a viewer which represents each rotated, equilibrated, and re-
docked structure as a single sphere. The location of this sphere in the three-axis
coordinate system shown in the viewer corresponds to the σy⋅σx⋅σz rotation angles
applied to obtain the structure. The color of the sphere corresponds to the estimated free
energy of ligand binding for that conformer, with red=high and blue=low energy. With
this viewer it is easy to see regions of pitch-yaw-roll space which contain low-binding-
energy conformers.
sRMSD benchmarking
Once the alternate conformers have been generated by rotation, equilibration, and re-
docking, we are faced with the problem of determining how distant these are from the
known target conformer, in our case the protein from the co-crystallized complex.
Simply computing the RMSD between the Cα atoms of the predicted structure and those
of the co-crystallized protein is not effective, since M is undergoing significant changes
but S is not. Maiorov et al. instead used a “static” root-mean-square deviation (sRMSD),
defined as the RMSD of the Cα atoms in M, provided the Cα atoms of S are optimally
superimposed. We use the same measure in the current work.
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