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Rigid docking was evaluated using both standard precision Glide and extra precision Glide scores [ 26].
Bubbles appear in the tissue and the lymphatic collectors and an operating microscope (Stemi 2000, Carl Zeiss Pty. Ltd. Germany) is used to identify and cannulate the lymphatic vessels with a 30-gauge needle (Precision glide needle: Becton Dickinson & Co., USA).
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Flexible receptor docking was implemented using a multistage induced fit docking protocol [ 27], where the final scoring was performed using the extra precision (XP) Glide scoring function [ 26] and an MM-GB/SA rescoring function [ 28– 328.
Dancers, shifting seamlessly between the weight of street dance and the elevation and precision of ballet, glide in harmony to classical music.
Due to the fact that the natural products tended to be large compounds with many rotatable bonds, we used standard precision docking in Glide and the default genetic algorithm settings in GOLD rather than high-throughput or speeded-up screening settings, and we increased the sampling by saving 20 poses for each compound.
The docking calculations were performed using the XP (extra precision) mode of Glide.
The identified hits were validated using different strategies, such as Glide Standard precision, extra precision, E-model energies and receiver operating curve (ROC).
LigPrep generated 5,636 3D structures with variations in, e.g., tautomeric and ionic form, which were docked flexibly in standard precision-mode in Glide (Glide version 5.6.107) to the generated receptor grid of each of the five-protein 3D structures.
Subsequently the rigid receptor docking was performed with the extra precision mode of the Glide 5.7 Ligand Docking application.
Also the orientation and the ligand protein interactions of the top hit molecules with MS DNA gyrase B subunit active site were investigated applying extra precision mode (XP) of Glide.
The low value of the root mean square deviations (ranging from 0.725 to 1.820 Å) between the starting complex structure and the energy minimized final average complex structure suggests that the Glide Extra Precision (XP) derived docked complexes are in a state of near equilibrium.
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