1. Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships 
Fan Zheng, Jian Zhang, Gevorg Grigoryan 
Structure 
Volume 23, Issue 5, Pages (May 2015)
DOI: /j.str
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2. Structure 2015 23, 961-971DOI: (10.1016/j.str.2015.03.015)
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3. Figure 1 The Procedure for TERM-based Analysis of a Structural Model
Each residue defines a TERM (two examples shown on the left, 1). Each TERM is subjected to a structure-based search against a non-redundant subset of the PDB, with close matches revealing the natural abundance of the TERM and its sequence preferences (superposition of close matches and resulting sequence logos shown for the same TERM examples in the middle, 2). This information is integrated to produce per-residue structure scores, shown mapped onto the model on the right (3) in blue-to-red false color (reflecting low to high scores, respectively). Superimposed in green is the native structure; low-scoring regions correspond to poor predictions. See also Figures S1 and S7.
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4. Figure 2 Structure Score Correlates with Model Accuracy
Plotted are model GDT_TS scores (x axis) versus total structure scores (y axis). Each of the first 41 panels includes models for one target (target ID indicated on each plot), while the bottom right-most panel combines models from all targets. See also Figures S2 and S3, and Table S1.
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5. Figure 3
A Representative Example Showing the Performance of Structure Score on Models of Varying Accuracy for a Given Target (TR644)
(A–C) Three models of increasing accuracy are shown superimposed onto the native structure (green). Models are colored by residue structure scores; the color scale is indicated on the bottom right. See also Figure S8.
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6. Figure 4
Per-Residue Structure Scores Correlate with Structure Prediction Error
The latter is defined as ln(σloc+σglob), where σloc and σglob are local and global structure prediction errors, respectively. Each circle represents a single residue (>52,000 residues in the dataset), and circles are colored by data density for clarity. The black line shows the median prediction error as a function of residue structure score.
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7. Figure 5 Structure Score Identifies Poorly Predicted Regions
Left, right, and middle pie charts correspond to residues with structures scores in the top 25th percentile, bottom 25th percentile, and those in between, respectively. Pie chart segments illustrate the fraction of residues, in each case, falling within different GDT subregions, as indicated. See also Figure S4.
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8. Figure 6
Despite Being Sensitive to Incorrectly Predicted Structures, Design Score Is Robust to Local Differences between NMR and X-Ray Structures
Each dot represents a single residue. Most of the outliers are attributed to two regions shown; gray and black dots correspond to structural regions shown on the top and bottom, respectively, to the right of the plot. In the region of difference, the X-ray and NMR structures are denoted with black and gray, respectively. See also Table S2.
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9. Figure 7
The Relaxed State of α1-Antitrypsin Is More Compatible with its Sequence than the Stressed State According to TERM-based Analysis
(A) Pre-cleavage stressed (left) and post-cleavage relaxed (right) states of α1-antitrypsin, as exemplified by structures PDB: 1QLP and 1D5S, respectively. Color and cartoon thickness represent structure score differences (relaxed minus stressed; color scaling indicated). RCL, reactive center loop.
(B) Structure score differences plotted against residue number show two regions of most prominent change (dotted lines denote the level of significance; see Experimental Procedures).
(C) Although the two regions are not in direct contact, their structural rearrangements are coupled. See also Figure S5.
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10. Figure 8
Structural Plasticity of Ubiquitin Borne Out in TERM-based Analysis
(A) Mapping of structure scores in the context of several structures of ubiquitin representing the open-to-closed conformational.
(B) Structure score color scale mapped onto the sequence of ubiquitin; same color bar as in (A) applies. See also Figure S6.
Structure  , DOI: ( /j.str )
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