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The model with lowest DOPE score and allowed backbone angles was refined and minimized using Rosetta minimization program [ 74].
The full-atom ligand structure was then minimized using the Q-MOL small molecule minimization protocol.
Each rotamer was minimized using 500 steps of steepest descent minimization.
Each cell was minimized using 100 K steps of the default minimization algorithm included in NAMD.
The molecules were minimized using the OPLS-2005 field field.
Energy of molecule was minimized using by PRODRG server [39].
The energy consumption was minimized using the SQP method.
An objective function is minimized using a gradient method.
Further, compounds were minimized using GAMESS [36] RM1 semi-empirical molecular orbital model.
Then, these 1290 molecules were minimized using the MMFF94 force field implemented in SYBYL [17].
E is minimized using simulated annealing algorithm (Kirkpatrick et al. 1983).
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