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D3RMSD_aligned is not to be confused with sRMSD (formally defined later), which is
computed for domain 3 in the holo vs. predicted proteins aligned on domain 1.
Holo, redocked, predicted, starting, apo, and aborted structures
For each protein studied, we discuss three protein-ligand configurations (Figures 3-5).
The holo structure is the crystallographically determined structure of the enzyme bound
with ligand, which we use as a gold standard, and which would presumably be unknown
in a practical situation. The redocked structure is the structure of the protein only
extracted from the holo complex, with the ligand atom positions determined by docking.
The starting structure is the protein structure which would be known in practice and
which is used as a starting point in our analysis. In many cases this will be the apo
structure and so in this work the two terms are used interchangeably. The generated
ensemble is the set of all structures generated by rotating M and possibly equilibrating
and docking. The predicted structure is the conformer chosen from the generated
ensemble as the best approximation of the holo structure. In the ligand docking example
explained here, it is selected based on the described fitness function. This is shown
graphically in Figure 5.4.d-f. The aborted structure is one that could not be generated for
one of two reasons: (1) the rotation was effected but the steric strains generated were too
large and so the equilibration step failed to converge, or (2) the equilibration converged
but the drift left the structure not in the targeted cell (we will definet this term below) but
in a neighboring one, even after two successive attempts at rotation and equilibration. In
both cases the rotated but unequilibrated structure in the target cell was marked as
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