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L may be qualitatively predictive of the actual structure of the complex.
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70
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The other low-energy docked complexes (defined as those having scoring energies within 4 kcal/mol of the lowest energy complex) did not differ greatly from the lowest-energy complex shown in Figure 6. We performed a second round of docking calculations starting with an orientation of 24 in the BH3-binding pocket of Bcl-xL that was rotated ∼180° (i.e, the positions of the N-terminus and C-terminus were swapped) relative to that shown in Figure 6. This experiment resulted in low-energy complexes that had scoring energies > 30 kcal/mol higher than complexes from the first round. All of the low-energy complexes from the second round, however, showed 24 oriented in the BH3-recognition cleft in a manner similar to that in Figure 6 i.e, 24 had rotated ∼180° back to the orientation found in the first round of docking, but side chain/Bcl-xL contacts were diminished due to translation of the oligomer out of the Bcl-xL c
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L cleft.
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