Comparison of Homology-Based Validation Schemes. Performance of the scoring scheme ('PRIMOS Score') in comparison to two conventional approaches (named 'FASTA Binary' and 'PSI-BLAST Binary' here), where a PPI is deemed as biologically relevant as soon as a single homologous PPI is found below a certain E-value. GSP PPIs comprised all PPIs from the Combined data set, the Random data set was used for the GSN PPIs. For the two binary schemes, we used FASTA and PSI-BLAST, respectively, to identify homologous PPIs and calculated the TPRs and FPRs as the fraction of GSP PPIs and GSN PPIs that had at least one homologous PPI below a sliding E-value threshold, ranging from 10-300 to 10 in this figure. Black rectangle: parameter settings from Saeed and Deane . Black circle: parameter setting used by Patil and Nakamura . The area under the curve (AUC) is 82%, 83%, and 86% for the FASTA, PSI-BLAST, and PRIMOS curve, respectively.