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Table 2 Identification experiments using GO-PDB data

From: Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology

Seq. Similarity Pos/Neg
(% Pos)
Methodolgy AUC TPR-0 TPR-1% TPR-5%
   P-1 0.67 1.32 1.32 23.68
   PS-1–8 0.75 7.89 15.79 36.84
50%
(Figure 1)
76/215
(21%)
PF-1 0.53 1.32 5.26 9.21
   BLAST 0.63 0.00 31.58 39.47
   PH-3 0.70 7.89 10.53 30.26
   PSH-3–9 0.64 11.84 18.42 31.58
   P-3 0.68 12.28 14.04 30.70
   PS-1–9 0.77 5.26 7.89 41.23
90% 114/353
(24%)
PF-3 0.64 0.00 7.02 19.30
   BLAST 0.59 0.00 33.33 46.49
   PH-3 0.70 8.77 20.18 39.47
   PSH-3–8 0.74 15.79 19.30 36.84
   P-3 0.96 57.27 76.48 83.12
   PS-3–9 0.96 53.14 64.99 82.76
0% 557/1443
(28%)
PF-3 0.89 25.85 32.50 63.38
   BLAST 0.73 0.00 60.14 66.97
   PH-1 0.90 17.59 25.49 66.07
   PSH-3–8 0.91 39.50 55.30 71.10
  1. The results (including Figure 1) of DNA repair protein identification experiments using proteins drawn from the Protein Data Bank containing the DNA repair Gene Ontology. "Pos/Neg" shows the respective numbers of repair proteins and nuclear non-repair proteins. Column meanings are similar to Figure 1. For each sequence similarity dataset, the top performing method for each metric is underlined (unless a tie exists in more than half of the classifiers).