Figure 1.
Percentage of Multidomain Chains with a Given Number of Component Domains
Figure 2.
Example of a Multidomain Protein (PDB: 1cg2) Chain Containing a Discontiguous Domain
Domain two (blue) is inserted between two segments of domain one (red).
Table 1.
Percentage of Correct Folds Identified by GT and DDP
Figure 3.
ROC (True Positive Rate Versus False Positive Rate) Curve Plotted for Different Structural Comparison Methods Based on the SAS, Where a Positive Match Represents a True CATH–SCOP Fold Match
TPR, true positive rate; FPR, false positive rate.
Figure 4.
Graph of the Percentage of Correct Folds Matched Against the Ranked Native Score for the CATH–SCOP Dataset
Figure 5.
Comparison of Alignment Quality of Domains Adopting the Same CATH Fold Using Two Geometric Scoring Schemes
(A) Percentage of correct fold pairs for a given SAS threshold.
(B) Percentage of correct fold pairs for a given SiMax threshold.
Table 2.
Residues Aligned by Each Method Relative to DDP for All Genuine Fold Matches
Figure 6.
Average Number of Aligned Residues per SAS
Figure 7.
Graph Showing How the Alignments of Each Method Compared with Manually Validated BAliBASE Alignments
The higher the curve (or the curve with the greatest area underneath) represents the method that most agrees with the manually curated BAliBASE alignments.
Figure 8.
Comparison of GT and DDP Scores with SVM Score for Assigning Domains to Multidomain Chains
Figure 9.
Percentage of Domain Assigned (Blue) and Percentage of Domain Boundaries within Ten Residues of Verified Boundaries (Pink) at a Range of SVM Score Cutoffs
Figure 10.
Domain Coverage Versus Quality of Domain Boundaries
Figure 11.
Percentage of Domains with Correct Domain Boundaries (within Ten Residues) When Varying the Number of Representatives Taken from Each Superfamily in the Targeted Fold Groups
Figure 12.
Graph of the Percentage of Correct (within Ten Residues) Domain Boundaries against the Sequence Identity between the Assigned Region and the Matched Domain
Figure 13.
Superposition of the Catalase HPII (PDB 1iph; First Domain of Chain A) as It Is Classified in the CATH Database and Its Match to Bovine Beta-Lactoglobulin, Coloured Red, (PDB 1beb; Chain A), the Closest Relative Identified by CATHEDRAL
Figure 14.
Flowchart of CATHEDRAL Algorithm for Assigning Folds and Domain Boundaries to Protein Chains