Fig. 1.

(A) Strategy for constructing a multidomain selectivity model for mouse PDZ domains. Protein microarrays were used to test all possible interactions between 157 mouse PDZ domains and 217 genome-encoded peptides. Array positives were retested and quantified by FP, thereby correcting array false positives. The resulting data were used to train a predictive model of PDZ domain selectivity. The model highlighted putative array false negatives, which were tested by FP, and the corrected data were used to retrain the model. After three cycles of prediction, testing, and retraining, the refined model was used to predict PDZ domain–protein interactions across the mouse proteome. (B) Representative images of protein microarrays, probed with fluorescently labeled peptides. PDZ domains were spotted in quadruplicate in individual wells of 96-well microtiter plates. (Four wells were required to accommodate all of the domains.) The red images (Cy5) show the location of the PDZ domain spots. The green images show arrays probed with a promiscuous peptide derived from Kv1.4 (left) and a selective peptide derived from ephrin B1/2 (right). (C) FP titration curves obtained for the array positives identified in (B).