From complete cross-docking to partners identification and binding sites predictions
Fig 2
Predictive performance on the PPDBv2.
(A) AUC values computed for the whole dataset and for the different functional classes. For each protein, we consider one “true” cognate partner, defined from the PPDBv2 annotations. The results obtained with CCD2PI are indicated by the blue curve. For comparison, we also show the results reported in [53] in purple. The areas in grey tones give the discriminative power reached when exploiting the knowledge of the experimental interfaces, using either our default parameters (in light gray) or parameters optimized for such interfaces (in dark grey, see also Materials and methods). The number of proteins in each subset is indicated in parenthesis. (B) Proportion of proteins with at least one known partner found in the top 20% of CCD2PI predictions, for each subset. The known partners are defined from the PPDBv2 annotations (in blue) or are inferred from complex PDB structures involving the proteins from the set or their close homologs, sharing more than 90% (in dark red) or 70% (in orange) sequence identity. The grey bars give baseline expected values based on the number of known partners (see Materials and methods). (C) NII matrices computed by CCD2PI. The proteins are ordered on the x-axis such that the receptors (e.g. antibodies) appear first, and then the ligands (e.g. antigens). They are ordered on the y-axis such that the cognate pairs annotated in PPDBv2 are located on the diagonal. The orange tones highlight the experimentally known interacting pairs (annotated in the PPDBv2 and transferred by homology). AA: antibody-antigen, ABA: bound antibody-antigen. EI: enzyme-inhibitor. ER: enzyme with regulatory or accessory chain. ES: enzyme-substrate. OG: other-with-G-proteins. OR: other-with-receptor. OX: others.