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This method enabled us to discriminate between significantly scoring structures due to their high frequency and those that are truly overrepresented and therefore a true positive hit.
Raloxifene docked well to one of the Hsp90 structures (pdb code 1uyf), but not to the best 2 scoring structures for tamoxifen (pdb codes 2ior and 1uy8).
Similar to scoring structures that favor overlapping alignments, PAT filters out local alignments.
However, the search for high scoring structures is not trivial.
Next, we analyze the accuracy of the best scoring structures in the ensemble.
Finally, the best scoring structures are refined to locally optimize the fit between assembly and component density maps.
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The total score reflects the scoring structure indicated in the manual, that is the six domains are summed, and then the domain totals are summed together to make the total score.
This study builds on previous evidence that established the domain and scoring structure of the HDQ and confirmed the validity of the six domain structure with adults living with HIV in Ontario [ 26, 46].
Corresponding plots of HADDOCK score vs RMSD (to the lowest scored structure) for each of the dimers are shown below the structures.
Plots of the HADDOCK score vs RMSD (to the lowest scored structure, left) and a histogram of restraint violations (right) illustrate this.
The current study demonstrated that sleep quality in TMD patients, as assessed by the PSQI, is a unidimensional scoring structure.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com