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At the end of each equilibration the ligand is removed from the structure file and then
docked again to the protein using AutoDock 3[98]. The docking code reports multiple
poses (docked ligand atomic positions) with corresponding free energies of binding; we
record the lowest of the latter. The corresponding ligand coordinates are then appended
to the protein structure file.
Computing the radius of gyration, stability, and domain distortion.
The radius of gyration is a standard quantity which was computed taking into account
only the masses of the Cα atoms of the protein, according to the definition:
2 1
Rg =
N
N
#
k=1
( ) 2
r k " r mean
where N = number of residues, and rmean = centroid of the Cα atoms.
The stability , or free energy of folding, of the structure is estimated using the FoldX.
The latter is a force field empirically fitted by Guerois et al. using a database of
mutationally induced changes in protein stability[122].
Domain distortion is the sum of two terms defined as follows. D1RMSD_aligned is the
RMSD between domain 1 of the starting structure, and domain 1 of the predicted
structure. Similarly, D3RMSD_aligned is the corresponding quantity for domain 3. In
both cases the domains were optimally aligned prior to computing RMSD.
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