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. Author manuscript; available in PMC: 2017 Jan 15.
Published in final edited form as: Methods. 2015 Sep 30;93:41–50. doi: 10.1016/j.ymeth.2015.09.026

Figure 4.

Figure 4

Ligand docking of RXRα. A, Superimposed holo (gold) and apo form (green) of RXRa. The cognate ligand is colored in magenta. B, The top scored conformation of ZINC03834071, which is ranked 2nd(holo form) and 1st(apo form) by PL-PatchSurfer. Matched patch pairs of the pocket and the ligand are shown in the same colors. C, the docked structure of an active compound, ZINC01539579, which was ranked the 1st(holo form, left, pink) and the 8th(apo form, right, white) by AutoDockVina. The bound structrure of the compound is shown in magenta. D, the docked structure of ZINC03834076, which was ranked the 1st(holo form, left, cyan) and the 84th(apo form, right, orange) by DOCK6.