Figure 5.

Energy landscape of the RXR LBD dimer. (A) A plot of E₁₂ versus RMSD. A total of 58,480 configurations from CGMD simulations are shown in black dots, where R_max = 100 Å, R_c = 45 Å, and R_min = 0 Å were used in the PPR scheme. (B) Front view of the energy globe colored by E₁₂. We used a total of N_f = 589 clusters (also shown in blue dots in A) after the two-step clustering. Four representative conformations (a–d) are shown on the globe, where conformation (a) resembles the crystal structure (64). (C) The decomposition of hydrophobic (white bars) and electrostatic (gray bars) energies from E₁₂ for each conformation (a–d).