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. Author manuscript; available in PMC: 2018 Jan 29.
Published in final edited form as: Biochem Biophys Res Commun. 2016 Dec 26;483(1):203–208. doi: 10.1016/j.bbrc.2016.12.165

Fig. 2.

Fig. 2

An example of the open-pull-close pulling path and the pulling centers (purple spheres/disks) on the ligands. In the top panel, the protein (CRBP1) is shown as cyan ribbons and the ligand (RTL) in purple licorice. The blues spheres indicate the four pulling centers on CRBP1. In the bottom panel, the ligands are represented with licorices (colored by atom names: carbon, cyan; hydrogen, white; nitrogen, blue; oxygen, red; sulfur, yellow). (A) Retinol (RTL). The pulling centers on this ligand are atoms C6 and C11. (B) and (C) Benzylacetate (J0Z). The pulling centers on J0Z are, respectively, atoms CAJ and CAG in simulation Set I and atoms CAJ and CAC in Set II. (D) 2-Nitrothiophene (265). The pulling centers on this ligand are atoms CAG and NAH. (E) Benzene (BNZ). The pulling center is the center of mass of this ligand.