Geometry ligand-receptor interactions

Tallarida, R., Further characterization of a control model for ligand-receptor interaction Phase plane geometry, stability, and oscillation, Annals of Biomedical Engineering, Vol. 18, 1990, pp. 671-684. 

Much more inFormation can be extracted From multiple complexed ligand structures. With these aggregate data, the binding geometry with receptor sites becomes clear, and the important interactions can be identified and ranked. The vectors oF these selected interactions can be Formulated into the 3D query with reasonable confidence both oF their occurrence and oF their accuracy. Lone pairs or sprouted hydrogens From these Functional groups can then serve as the root attachments For excluded volumes which represent the site atoms involved with each interaction. Conformational analysis of the receptor site and ligands, and the variability with which each site residue may be located in each complex, can be converted into tolerance on a per-residue basis which may be associated with the excluded volume constraints. 

Fig. 15. Schematic representation of a planar, tetrahedral, octahedral and double-helical arrangement of external interaction sites (arrows) on ligands organized around metal ions of given coordination geometry in metallo-exo receptors a linear strand is also shown.

---