Sensitivity and specificity of MLR and ZRANK methods evaluated on test dataset (44 native-like and 633 decoy structures). (A) Effect of window size on prediction accuracy. The window size represents the number of predicted positives. Prediction accuracy (or sensitivity) is determined by the number of test case structures (44 in total) correctly predicted. The rmsd threshold used for clustering ligand conformations was varied (3 Å, 5 Å, and 10 Å), and its effect on prediction accuracy was analyzed. (B) ROC curves at rmsd cutoffs 3 Å, 5 Å, and 10 Å for MLR and ZRANK predictions. The area under ROC curves at rmsd cutoffs 3 Å (MLR, 0.948; ZRANK, 0.862), 5 Å (MLR, 0.95; ZRANK, 0.718), and 10 Å (MLR, 0.943; ZRANK, 0.717) indicate that MLR is more efficient at recognizing native-like structures.