Fig. 1

Graphical pipeline for building HIPPO as a collection of four histogram sets (\({\mathcal{H}}\)). a Transition from a protein-RNA complex to a protein-ssRNA complex with ssRNA that is at least 3 protein-bound nucleotides long. This step was achieved using ProtNAff. b Creation of a pool of labelled docking pose using ATTRACT. Each protein-fragment case of protein-ssRNA complex is docked and each docking pose is labelled as near-native or non-native. c Construction of the distance arrays, refinement of the distance arrays and derivation of the histogram set \({\mathcal{H}}\) from refined distance arrays. The frequency of occurrences of individual bead-bead distances within a single pool of docking poses are captured within distance arrays, one array per each pair of bead types. c1 Close-up of contacts between RNA bead j = 1and protein bead i = 1 and j = 15. c2 An intuitive schema of the distance array for the pair of bead types (i = 1; j = 1) is shown as an expanded plot. The distance ranges are shown on the x-axis, and the numbers of occurrences of the distances are shown on the y-axis. For each distance range, the number of occurrences for the near-native poses is displayed as a blue bar, and for the non-natives as a red bar. The blue dashed line from c1 to c2 shows the contribution of the contact to the near-native distance array, range2. The other distance arrays (for other pairs of bead types) are not shown (collapsed). c3 An intuitive schema of the refined distance array for the pair of bead types (i = 1; j = 1) is shown as an expanded plot. Due to the relatively low number of near-native contacts in range1, it is merged with range3, forming a new range1^*. The following range3, which contains a sufficient number of near-native contacts, remains unchanged and is renamed as range2^* to preserve the range order. Finally, range4, which also contains an insufficient number of near-native contacts, is merged with range5 to form a new range3,*. c4 An intuitive schema of the histogram set \({\mathcal{H}}\), derived from the refined distances arrays, which are in turn built from the pool of the docking poses of the case1. A histogram for the pair of bead types (i = 1; j = 1) is shown as an expanded plot, other histograms are collapsed. d Schematic pipeline of the partitioning algorithm, employed to derive a collection of four histogram sets out of all sets