MOLECULAR SPELUNKING: AutoDock Vina evaluates a receptor’s entire binding pocket at once to find a docking site (lowest-energy binding) for a ligand of interest. The deepest part of the pocket (the actual binding site for auxin shown at the bottom of (1) naturally has a low energy requirement, and this is where, in the case of tryptophan (2), the software suggests a docking site. But by forcing the software to move in incremental steps—starting at the mouth of the pocket and moving inward—TomoDock finds an interaction of tryptophan with residues farther up the pocket (3) that prevents deeper entry. In the case of auxin, however, TomoDock finds the same binding site as that found using AutoDock Vina (step-wise progress of TomoDock shown in (1).© GEORGE RETSECK
Auxins are a family of small-molecule hormones that control growth and development processes in plants. They are also components of widely used herbicides. In a drive to extend the agricultural and horticultural applications of these hormones, scientists are attempting to design new synthetic auxins. But to do so, they must understand the nitty-gritty of how an auxin molecule binds to it receptor, says Richard Napier of the University of Warwick in the U.K.
Napier’s team uses docking software to simulate auxin binding. But there’s a problem: the software also allows molecules to dock that, Napier says, are known not to bind in reality—such as auxin’s close relative tryptophan. “Getting false positives out of docking [analyses] is absolutely part of the deal,” he says. “Docking is ...
