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1.
Figure 6.

Figure 6. From: How well can the accuracy of comparative protein structure models be predicted?.

Flowchart depicting the steps to predict the RMSD and NO3.5Å of an input comparative model.

David Eramian, et al. Protein Sci. 2008 November;17(11):1881-1893.
2.
Figure 3.

Figure 3. From: How well can the accuracy of comparative protein structure models be predicted?.

Receiver operating characteristic (ROC) curves for fourfold assessment classifiers: the predicted native overlap (solid black line); the normalized DOPE score (dashed black line); the GA341 score (solid gray line); and the sequence identity shared between the target and the template (dashed gray line). For each measure, the area under the curve is noted. A model was defined as having the correct fold if NO3.5Å ≥ 0.30.

David Eramian, et al. Protein Sci. 2008 November;17(11):1881-1893.
3.
Figure 5.

Figure 5. From: How well can the accuracy of comparative protein structure models be predicted?.

Examples of successful accuracy predictions where the sequence identity shared between the target and template was less than 12.5%, and yet very accurate models were constructed. Relying upon the individual features alone, neither model would be assessed as being very accurate, yet the weighed combination of these features using the model-specific assessment protocol leads to accurate assessments. In both images, the native structure is colored red and the model is blue. (A) Sequence from murine neuroglobin (PDB code 1q1fA) modeled using 1it2A as a template. (B) Sequence of 4-hydroxybenzoyl CoA thioesterase (1q4tA) modeled using 1s5uA as a template.

David Eramian, et al. Protein Sci. 2008 November;17(11):1881-1893.
4.
Figure 2.

Figure 2. From: How well can the accuracy of comparative protein structure models be predicted?.

The relationships between the actual NO3.5Å and sequence identity (A; r = 0.54); the normalized DOPE score (B; r = 0.71); and the predicted native overlap (C; r = 0.86). In each plot, the diameter of a bubble represents the number of examples contained in the 2D bin indicated by the x- and y-axes. The bubble size is comparable between the different plots. Additionally, the median value for each bin is depicted by the solid line, where the upper and lower error bars indicate the third and first quartile values, respectively. (D) The relationship between the predicted and actual RMSD (r = 0.84).

David Eramian, et al. Protein Sci. 2008 November;17(11):1881-1893.
5.
Figure 4.

Figure 4. From: How well can the accuracy of comparative protein structure models be predicted?.

Relationship between structure-derived properties and the predicted accuracy for 25,000 randomly selected models of length 100–200 amino acids. (A) The percentage of correct neighborhood (solid line) is plotted versus the sequence identity shared between the target and the template used to construct the model (r = 0.57). The solid line indicates the median value for the bin; the upper and lower error bars indicate the third and first quartile values for the bin, respectively. The columns indicate the fraction of examples that are contained in each bin (right y-axis). (B) Relationship between the predicted native overlap and the neighborhood accuracy of a model (r = 0.82). (C) The percentage of exposed residues correctly modeled as exposed versus sequence identity (r = 0.56). (D) Percentage of exposed residues correctly modeled as exposed versus predicted NO3.5Å (r = 0.65).

David Eramian, et al. Protein Sci. 2008 November;17(11):1881-1893.
6.
Figure 1.

Figure 1. From: How well can the accuracy of comparative protein structure models be predicted?.

Properties of the 580,317 model testing set (A–D). The y-axis on the left indicates the number of models that fall into the corresponding bin indicated by the x-axis. The line and right y-axis correspond to the cumulative percentage of total models having the appropriate feature. (A) The global sequence identity shared between target/template alignments of the test set. Approximately 80% of the models are from alignments in which the target and template share less than 30% sequence identity. (B) The length distribution of models in the test set (median = 111 amino acids). (C) The Cα RMSD distribution of the models, with a bin size equal to 2.0 Å (median = 7.0 Å). (D) The native overlap distribution, calculated using a cutoff of 3.5 Å (median = 0.46).

David Eramian, et al. Protein Sci. 2008 November;17(11):1881-1893.

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