Figure 5

PDZ-peptide contact and interaction prediction. (A) Residues predicted on PDZ domain are mostly located in the peptide binding site. Spacefill indicates PDZ domain and colored spacefill indicates PDZ residues predicted by RMRCM to interact with the peptide; ball-and-stick indicates peptide that interacts with the PDZ domain. Colors on the peptide indicate with which residues with corresponding colors on the PDZ domain those residues are predicted to connect; in one case, a residue on the PDZ domain obtains two colors (green and orange) because connections are predicted with two peptide residues. In some cases (e.g., blue residues) the predicted connections are between residues which are contacting each other; in other cases (e.g., orange residues) this is not the case, although the residues predicted on the PDZ domain are still relatively close to the peptide. Two additionally predicted residues on PDZ are at the backside of the molecule and are not visible. (B) Prediction of C. elegans PDZ-peptide interactions using human interaction data as training set. AUC values for C. elegans PDZ-peptide interaction prediction based on human interaction data (y-axis) vs. binding site identity of the C. elegans PDZ sequence with the best-matching human sequence (x-axis). Lines indicate randomly expected AUC (0.5) and binding site identity above which good prediction performance is obtained (0.6).