Fig. 3

Evaluation of the intrinsic disorder predisposition of PRAME. A. Per-residue intrinsic disorder profiles generated by RIDAO that assembles the outputs of PONDR® VLXT, PONDR® VL3, PONDR® VSL2, PONDR® FIT, IUPred_long and IUPred_short. The mean disorder profile (MDP) of the protein is calculated by averaging the disorder profiles of individual predictors. The light pink shade represents the MDP error distribution. The thin black line at the disorder score of 0.5 is the threshold between order and disorder, where residues/regions above 0.5 are disordered, and residues/regions below 0.5 are ordered. The solid red line at the disorder score of 0.15 is the threshold between order and flexibility, where residues/regions above 0.15 are flexible, and residues/regions below 0.15 are highly ordered. B. Per-residue intrinsic disorder profiles generated by predictors that performed better at a biannual blind test, Critical Assessment of protein Intrinsic Disorder prediction (CAID) [52]. These predictors are fIDPnn [53], AUCpreD [54], and SPOT-Disorder2 [31]. We also included the outputs of the Metapredict V2, which is a deep-learning-based predictor of consensus disorder scores [32]. Note that most predictors used in this study utilize the threshold of 0.5 to discriminate between ordered and disordered residues. The only exception is given by fIDPnn that utilizes the threshold of 0.3 for the same purpose (see right-hand Y axis in the plot B). Figure shows that PRAME is largely ordered protein but possesses elements of disorder throughout (i.e., regions comprising residues 1–15, 136–177, 330–376, and 510–509 are predicted as disordered by several predictors)