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Whether the instructor mentions it or not - practice the poses with the intention to focus.
Lastly, poses are ranked via consensus structure method, in which the poses with the top consensus scores of Shapegauss, PLP, Chemgauss2 and Chemgauss3 are retained, and all other poses are discarded.
Table 2 (full breakdown in ESI Table 4 †) reports the results of the free energy calculations based on the lowest energy docked poses, along with the RMSD of the poses with respect to the crystal ones and the binding free energy predicted by the docking scoring function for the same ligand.
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For residues with alternative positions, the pose with the highest occupancy was retained.
We define the epitome as the pose with the smallest pair-wise differences to other training sequences.
The rescoring of the poses was performed after a local optimization of the pose with 1000 iterations of the local optimizer.
A total of 30 docking poses were generated for each ligand and the pose with the lowest energy was selected for further studies.
The pose with the most favourable energy was selected and further refined by steepest descendent minimization.
The pose with the highest rerank score was retained in the workspace for detailed evaluation of the ligand binding at the active site cavity.
Repeat the pose with the left leg on top of the right.
Breath steadily and hold this position for five breaths and then repeat the pose with the other leg.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com