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The best conformations were selected on the basis of combination of binding energies as well as location of the docking.
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Docked conformations forming the coordination were generated for 104 out of 124 azaheterocyclic AIs, and 87 of the conformations were selected as the bioactive conformation.
Six conformations were selected from 380 results within a range of 6 kcal/mole above the global minimum.
One of the most frequent conformations was selected to represent the final conformation of the epitope in the MHC-I cleft.
The representative conformations are selected by clustering the MD sampled conformations.
Complementary protein conformations are selected from equilibrium of low-energy and higher-energy conformations.
The possible bioactive conformation was selected by a 3D-QSAR model.
The minimum energy conformation was selected in order to obtain the geometry optimization using the density functional theory (DFT).
For Vina, the lowest energy conformation was selected.
If alternative conformations exist for residues or atoms (e.g., residue 1 of THR in PDB 1CBN has two conformations), only the first conformation is selected.
The best isolates were selected for identification.
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