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. Author manuscript; available in PMC: 2011 Jun 1.
Published in final edited form as: Expert Opin Drug Discov. 2010 Jun 1;5(6):597–607. doi: 10.1517/17460441.2010.484460

Figure 1.

Figure 1

AutoLigand was used to identify potential binding sites to stabilize the homodimer of the transcription factor Max. The illustration shows the homodimer of Max (surface representation) bound to DNA (ball-and-sticks) and the small spheres show the optimal binding site identified by AutoLigand. The gray spheres have the highest affinity for carbon, the red spheres for hydrogen bond acceptors, and the cyan spheres for hydrogen bond donors. The search was done on a 1 Å grid spacing using only the protein coordinates (illustration created with PMV [56]).