We have produced a computer code, TomoDock, to create a tomographic docking application, and used it to discover how deep binding pockets present “security gates” that filter out some molecules while allowing others to reach their binding site. Thus, selectivity is more than docking. We use the plant hormone auxin and its receptor as a case study, and identify amino acids that are involved as molecular filters.

This image shows the protein surface of TIR1. Features of the binding pocket identified by TomoDock include the auxin engagement niche (purple), residues of the molecular filter (gold), IAA in transit (blue), and in its final docked (bound) position at the base of the pocket.	The movie shows how TomoDock predicts the movement of IAA as it moves into the TIR1 pocket. There is continual conversation between IAA and protein.

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Only auxins bind...