Figure 3
From: Prediction of TF target sites based on atomistic models of protein-DNA complexes
ROC plots of cognate site recovery in a set of random sequences for NarL, CRP, PurR and DnaA. Sensitivity (ordinate) and corrected specificity (abscissa) for the cognate binding sites recovery are plotted against in an assay in which the cognate binding sites are rescued from a dataset of non-sense random sequences, as explained in the Methods section. In this assay the W parameter is fixed to 1 while D, the linear weight of deformation costs assigned to indirect readout, is variable over its domain in the ROC plot analysis for NarL (A), CRP (B), PurR (C) and DnaA (D). In these charts the Area Under the Curve (AUC) is reported for each curve, corresponding to different assays with variable values of D. The PDB identifiers are NarL [1je8], CRP [1cgp], PurR [2pua] and DnaA [1j1v].