Exact(2)
β-Alanine was found to dock in two almost equally favored orientations.
Although the loop could adopt multiple orientations that could bring these residues in close proximity, without this constraint Rosetta favored orientations that placed Asp495 more distant from the acceptor lysine.
Similar(6)
Finally, the heme was modeled in the A orientation, which was shown to be the thermodynamically favored orientation for both NP7 and Met-NP7 Δ1 3). Met-NP7 Δ1 3
More importantly, the predicted N-dealkylation binding poses also suggested a crucial role of the 4-amino nitrogen atom, which was found to sit closely (3 4 Å) to the oxygen atom of the serine 119's hydroxyl group at the B C loop of CYP3A4 in an energetically favored orientation to form a strong hydrogen bond.
Without correction, the missing wedge is the strongest feature in individual subtomograms and tends to bias the alignment of any two given subvolumes, favoring orientations with maximum density overlap as opposed to optimizing the overlap of matching structural features (Fig. 7).
This effect is a direct consequence of an orientation-selective α → β transformation, favoring new orientations produced during nucleation and grain growth.
However, in some orientations, fracture or plastic slip are apparently preferred to martensitic transformation, and thus crystallography favors certain orientations if superelasticity or shape memory properties are specifically desired in zirconia ceramics.
It is shown that anisotropy favors particular orientations of the nucleus on the substrate.
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