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. Author manuscript; available in PMC: 2012 May 1.
Published in final edited form as: J Mol Graph Model. 2011 Aug 7;31:5–9. doi: 10.1016/j.jmgm.2011.07.008

Figure 3.

Figure 3

Predicted hydrogen-bond interactions with V2, a recently identified low-micromolar inhibitor of TbREL1. The visualization shown is representative of the default HBonanza-generated VMD visualization script, rendered with Tachyon. The ligand is shown in thick licorice, protein residues thought to participate in hydrogen-bond networks involving the ligand are shown in thin licorice, and the entire protein is shown in cartoon, colored according to secondary structure. Hydrogen bonds are colored in shades of green according to the frequency with which they appear in the many frames of the MD trajectory. The coloring ranges from white, those bonds present in 75% of the frames, to green, those bonds present in 100% of the frames.