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In case that the best conformation does not fulfill the matching criterion, the residue entry was only retained if the first alternate location has no overlap with the reference ligand.
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Although BAK adopts an oligomeric conformation after its release from BCL-XL, this conformation does not induce MOMP.
It is true that the ADP conformation does not support substrate and ClpP interaction.
These substitutions while efficient to stabilize the conformation do not partipate to the complex formation.
As expected, the latter conformation did not change during MD simulations.
Circular dichroism measurements proved that overall structural conformations did not change.
The addition of further conformations did not significantly improve the performance and could even deteriorate it.
The modeled APS2– is flexible during the simulation, but their conformations do not vary significantly.
CD44 antibody 1 and antibody 2, which do not recognize these CD44 conformations, did not enhance adhesion (Fig. 6A).
Second best does not lead to the best success.
Even though the Rosetta designed sequence represents an energy minimum for the scaffold conformation, this does not mean that this sequence cannot fold into a different conformation.
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