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The results revealed a preferred ligand-binding pocket in H4R, which would not have been identified using an unrefined homology model of the protein.
Comparing to the unrefined model and human AChE (hAChE), the refined model has different main-chain conformations in three adjacent loops of residues 70 77 (loop 1), 280 288 (loop 2), and 333 349 (loop 3).
In contrast to the unrefined model, the refined model has the thiol group of C286 interacting with W280 and Y333 via sulfur-aromatic interaction [17] and the guanidino group of R339 partially accessible to solvent.
Although some post side chain refinement models had worse Z-DOPE scores than unrefined models, they exhibited better stereochemistry (Additional file 13) and are therefore likely to be more accurate than the unrefined models.
In a blind test, this ab initio phase solution method resulted in significant improvement in structural resolution compared to that of the original unrefined models.
From Figure 2, it can now be safely assumed that structures scoring above 16 show native like properties and scores of bad, unrefined models are generally very low.
Excellent quality of the structure solutions after molecular replacement with the complete but unrefined models is evident from the Phaser statistics: TFZ = 9.0/LLG = 996 for 4.7 Å; TFZ = 14.2/LLG = 899 for 6.6 Å; and TFZ = 13.0/LLG = 795 for the 7.6 Å dataset.
"[Iggy]'s an unrefined intellectual, but totally intellectual.
Walken is a hawk and an unrefined bully.
He was an unrefined, flag-drawing liability as a fill-in starter in '08.
For rolling, any coarse decorative sugar works, as would Demerara or an unrefined sugar.
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CEO of Professional Science Editing for Scientists @ prosciediting.com