Figure 4
From: Modeling of the OX1R–orexin-A complex suggests two alternative binding modes
3D-representations for the docking pose clusters and scatter plots from multidimensional scaling, OX2R-based model. (A, C) Ten largest clusters; (B, D) Ten top-scoring clusters. In panels A–B, the TM1 is on the right. Multidimensional scaling shows the clusters (colored; numbers refer to size ranking) in respect to the pool of docking poses (gray). Poses leaning towards the TMs 1–2 are shown in shades of red/magenta, poses leaning to the TMs 5–6 are cyan, blue or purple, and poses vertically in the cavity are orange, green or dark green (See Additional file 6 for all clusters and the color division). The coloring is consistent between 3D-representations and plots.