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Then, the Accelrys Discovery Studio 2.5 (DS 2.5) was used for the molecular docking selection.
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Fig. 3 Docking pose for selection of candidate residues related to ginsenoside Rd-hydrolyzing activity.
The disorder region can be defined better as a hard work for drug design than as a bad docking site for selection in our known.
Therefore, the disorder region should be defined as a hard work for drug design and not a bad docking site for selection.
But some references [ 41, 42] indicate that the interaction with the disorder region might cause lower side effect than with the widespread domain; thus, the disorder region cannot be defined as a bad docking site for selection.
All compounds were then viewed as docked on the receptor and manual selection was based on docking position to maximize diversity of docking locations on the EGFR dimer.
125– 127 The concept of "ensemble docking" usually requires the selection of a representative set of snapshots coming from a simulation and uses them as targets in normal docking procedures.
Although CFP or DsRed in the published docking lines allow positive selection of the attP site a major advantage to remedy accidental strain contaminations— they bar the possibility of using the same selectable markers for transgenesis.
In the second part we used FReDoWS, applying the selection feature, to execute selective docking experiments with the RFFR model of InhA-ETH complex with the same docking protocol used in the exhaustive test case.
Initially, selection of suitable docking program for our target of interest was possible by re-docking with GOLD, MOE, and Surflex programs.
For the selection of best docking program with respect to the current biological system, GOLD [41], MOE [42] and Surflex [43, 44] docking programs were employed.
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