Fig. 2

Comparison of TNF-α trimer and HIV-1 RT binding sites with ProCare. A Distribution of pairwise similarity scores (n = 195 × 3). Entries scoring above 0.47 (p-value = 0.05; threshold marked by the red dashed line) are considered similar according to a previous statistical analysis of 2 million pairwise alignments [17]. B Aligned residues of TNF-α (chain A: cyan, chain B: dark slate blue, chain C: cornflower blue; PDB code: 6OOZ) to HIV-1 RT (orange, PDB code: 1FKO) after rotation and translation of HIV-1 RT protein with the resulting ProCare alignment matrix. C ProCare alignment of efavirenz main fragment (light orange) in the TNF-α trimer pocket and PLANTS docking (transparent orange) in the TNF-α trimer pocket (PDB code: 6OOZ). Edge-to-face aromatic interaction with TYR59 of TNF-α chain A and hydrogen bond with TYR151 of TNF-α chain C are depicted by blue dashed lines