Secondary structure accuracy measurement

In protein secondary structure prediction, where a three-category (a, P, and coil or loop) prediction is made, the accuracy can be measured by a 3 x 3 accuracy table, as in Rost and Sander (1993). 

One key element in the performance analysis of secondary structure prediction methods is the proper selection of the accuracy measurement to be employed. Three different types of predictive accuracy measurements were used (Schultz and Schirmer, 1979) ... 

The standard measure for accuracy is Q3 defined as the number of residues correctly predicted divided by the number of residues. Q3 can also be computed for the residues of individual proteins Q3P or of individual secondary structures QH, QE, and QC. Other methods use certain types of correlation coefficients or take the type and position of secondary structure elements into account (proposed by Rost [168] and further developed for the CASP experiments [169]). One example is the SOV (segment overlap) score, i.e. the average over all secondary structure segments of the ratio of the overlap of predicted and true secondary segment and the overall length of the two segments. 

Apparently alacrinite is also a low-temperature polymorph that simply stacks differently as well (Burns and Percival, 2001). We are not aware of any thermodynamic data on either pararealgar or alacrinite but since the crystal structures are identical except for molecular stacking, the free energies should be very similar to within the accuracy of calorimetric or solubility measurements. Duranusite and dimorphite (and possibly uzonite) are secondary alteration products of realgar (Clark, 1972 Marquez-Zavalia et al., 1999). 

The quality of the calibrators and the calibration procedure used are major factors in determining the reliability of the analytical values obtained with a procedure. To appreciate the problems in standardization and calibration, knowledge of the overall structure of an accuracy-based measurement system is necessary. Uriano and Cali and Tietz have defined a hierarchy of analytical methods and reference materials that shows the relationship between reference materials and analytical methods of different quality. Figure 19-7 illustrates how "field methods are related to "reference methods by secondary reference materials and how reference methods are related to definitive methods by primary reference materials. ... 

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