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The noncrystallographer can assess model quality by carefully reading original publications of a macromolecular structure.
A more impartial way is to assess model quality by comprehensible measures like accuracy, clarity, completeness, conciseness, or consistency.
Evaluation of model quality by QMEAN indicates that the regions of poor quality are located at the N- and C-terminal portion of the structure (Figure S1).
The most "parsimonuous" was selected by mean of the Akaike Information Criterion AICC), which provides a measure of model quality by simulating the situation where the model is tested on a different data set.
ProSA web analysis also showed the protein model quality by plotting energies as a function of amino acid sequence position.
The structural data for the selected chain are then analyzed for local model quality by the perl script, which then calls the V3D software.
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Table 4 compares the model quality predicted by SP3, SP4, and SP5.
Accuracy and specificity metrics are not influenced by the model quality λ or by the cutoff value χ; both metrics fluctuate around a value of 0.97-1.00 irrespective of the underlying model quality or applied threshold cutoff.
The model quality was determined by performing a linear regression between the modeled and experimental potential fields.
Model quality was assessed by the sensitivity, specificity, accuracy and area under the receiver operating characteristic (ROC) curve and the goodness of fit evaluated by the Hosmer Lemeshow statistic.
Remarkable improvement in the model quality was achieved by refinement with autoBUSTER through implementation of local structure similarity restraints (LSSR) [38] and manual building using Coot [40].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com