Fig. 5

Score distribution of pairwise comparisons between binding sites of TNF-α trimer and HIV-1 reverse transcriptase. Binding sites in asymmetric structures of TNF-α trimer (n = 3) were compared to binding sites of non-nucleoside inhibitors in HIV-1 reverse transcriptase (sc-PDB set, n = 122). Pairs with similarity measures scored above each method-specific threshold (red dashed line) were considered similar. For SiteAlign comparisons, pairs are considered similar in case the two distances (distance 1, distance 2) are below the recommended cut-off. For ProBiS, the threshold above which an alignment is considered significant is marked by the blue dashed line