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A fundamental assumption in implicit in this approach: structures that can obtain the binding geometry only at the expense of significant internal strain energy are not of primary interest as targets. Several arguments can be made to counter this assumption: (a) there are unpublished indications that many ligands in the Brookhaven Protein Data Bank appear to retain significant internal strain energy on binding; (b) the possibility that the net effect of binding to the receptor may be to stabilize ligand conformations that are less favorable in the unbound state; and (c) a preorganized ligand may not have a kinetic pathway to bind to its target. However, in the prospective design process, in which many good ideas must be prioritized into a few synthetic targets, it is a reasonable starting point to expect an energetic advantage for a ligand whose low energy conformation in the ambient milieu (in our case, aqueous pH 5.5 buffer) is very close to its optimal bound conformation in the target receptor.
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