Functional Differentiation of Proteins: Implications for Structural Genomics  Iddo Friedberg, Adam Godzik  Structure  Volume 15, Issue 4, Pages 405-415 (April 2007) DOI: 10.1016/j.str.2007.02.005 Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 1 Flowchart Illustrating the Rationale for Function-Driven Target Selection For each protein in a defined sequence space, determine whether the structure can be reliably predicted from the sequence. If the structure can be reliably predicted, but the function cannot be predicted to be the same as that of an already solved structure, then the protein is a target of interest. This complements the “new fold” strategy. The strategy discussed in this study is delineated by the dashed line. Structure 2007 15, 405-415DOI: (10.1016/j.str.2007.02.005) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 2 Distribution of FFAS03 Scores for Pairwise Alignments of Sequences from SCOP Histogram of the distribution of FFAS03 scores from two populations of protein sequences which were pairwise aligned, all-versus-all within each population. The white bars histogram shows the distribution of scores from alignments of proteins taken from different superfamilies, but in the same fold. The black bars histogram shows the distribution of scores from pairwise alignments of proteins in the same superfamilies. Structure 2007 15, 405-415DOI: (10.1016/j.str.2007.02.005) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 3 ROC Curves for All Superfamilies The performance of C4.5 on recognition of same and different superfamilies using all-versus-all on sequences taken from all folds (diamonds); sequences taken from folds with more than one superfamily (crosses); and sequences taken from folds with more than five superfamilies (squares). AUC, precision, recall, and population size are all given in Table 2. Structure 2007 15, 405-415DOI: (10.1016/j.str.2007.02.005) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 4 ROC Curves for Selected Folds Diamonds, TIM barrel fold (SCOP c.1.-.-); squares, immunoglobulin fold (b.1.-.-); crosses, flavodoxin-like (c.23.-.-). Structure 2007 15, 405-415DOI: (10.1016/j.str.2007.02.005) Copyright © 2007 Elsevier Ltd Terms and Conditions