Figure 3.

Edge distributions in the minimal ligand binding pockets (GREMLIN vs. null set) and Location of minimal ligand binding pocket residues in rhodopsin structure. The spatial organization of residues in the minimal binding pocket (A) B7 and the larger pocket (B) B6 as present in the rhodopsin structure (PDB id 1U19). Rhodopsin numbering along with Ballesteros-Weinstein numbering (superscript) is given for comparison with other GPCRs. For clarity only the binding pocket residues are shown along with bound RT (in magenta). The images were generated using PyMOL (Version 0.99rc6; webcite). In (C), the percentage of edges for GREMLIN (squares) and null set (diamonds) are plotted against the minimal ligand binding pockets sorted by their size. The bars indicate fold enrichment (values on secondary y-axis) of edges in GREMLIN over the null set

Moitra et al. BMC Biophysics 2012 5:13   doi:10.1186/2046-1682-5-13
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