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. 2018 Sep 29;115(9):1707–1719. doi: 10.1016/j.bpj.2018.09.021

Figure 4.

Figure 4

Structures from the lowest free-energy clusters. Ligand densities are shown for a set of 100 randomly chosen structures from the nodes identified in Fig. 3A. (A) The crystallographic pose is shown in red, and the median ligand pose is shown colored by atom type. Two residues are shown that are important for binding: Tyr97 and Asn140 for Brd4 and Tyr1901 and Asn1944 for Baz2B. The ligand density is determined using the VolMap tool of VMD and is shown at an isovalue of 0.1. (B) The RMSD distribution of the 100 selected poses to the crystal pose is shown for Brd4 (top) and Baz2B (bottom). To see this figure in color, go online.