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Figure 1 | BMC Bioinformatics

Figure 1

From: Variation of geometrical and physicochemical properties in protein binding pockets and their ligands

Figure 1

A set of Adenosine-mono-phosphate (AMP) ligands bound to non-homologous binding sites is shown. Each row displays different geometrical and physicochemical properties of the binding site and ligand respectively. From top to bottom are shown the variation of the ligand shape, the binding pocket shape, the hydrophobicity of the protein mapped on the ligand shape, the van der Waals potential and the electrostatic potential both again mapped on the ligand shape. The properties were ordered according to their average degree of similarity among the different binding pockets from highest to lowest from top to bottom. In addition the AMP binding pockets were ranked according to the similarity of their bound ligand to the AMP ligand of the Protein Data Bank [3] structure 1amu [4].

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