PDZ domain binding selectivity is optimized across the mouse proteome - PubMed (original) (raw)

Fig. 2

(A) Graphical view of the training-set data. K_d’s of FP-confirmed positives are represented by colors, ranging from high affinity (red) to low affinity (light blue). Array negatives are shown in black, and FP-confirmed negatives are shown in dark blue. Numerical values are provided in table S3. (B) Performance of the MDSM on the training set, with m set to 5. True positives are shown in red, false positives in green, true negatives in blue, and false negatives in yellow. (C) Graphical representation of the MDSM parameters, θ_i,p,q. Positive contributions to discriminative binding are graded from black to yellow, and negative contributions are graded from black to light blue. Numerical values are provided in table S4. Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr. (D) Tight clusters embedded in the bipartite interaction network between the 74 PDZ domains and the 217 training-set peptides. (E) ROC curves for three versions of the MDSM, obtained with the test set of 48 peptides. The best performance was obtained after smoothing over both PDZ domains and amino acids. The performance of each version of the MDSM with m set to 5 is indicated with an arrow.