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Physicochemical complementarity is commonly believedto be the driving force for molecular binding. The comple-mentarity for example of electrostatic potentials isregarded as the force that draws the ligand from the sol-vent into the binding site [1]. If this hypothesis is true, thesame ligand should encounter complementarity environ-mental properties in all proteins to which it binds. Wehave used our recently published ligand and bindingpocket matching algorithm [2] to test this commonassumption by searching for property distributions thatare similar for the same ligand bound to different pro-teins.

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