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. Author manuscript; available in PMC: 2019 Mar 7.
Published in final edited form as: Methods Enzymol. 2016 Jul 11;578:373–428. doi: 10.1016/bs.mie.2016.05.042

Figure 5.

Figure 5.

Ensemble docking of a drug substrate into the translocation lumen of P-gp. (A) MD simulation-generated ensemble of conformations used in molecular docking. Two pseudosymmetric halves of P-gp are colored in cyan and orange, respectively. Only 100 out of 1000 conformations used in ensemble docking are shown. A set of translocation path residues is shown to display the diverse side chain conformations represented by the MD-generated ensemble (inset). (B) Top 5 RMSD-based clusters of docked poses of the drug molecule are shown in different colors with P-gp in surface representation. One half of the protein is shown transparent to clearly show the clusters of the docked drug molecule.