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What should I do if I want to run a docking experiment, but my experimentally determined target structure doesn't have a bound ligand?

When working with an apo structure, it is important to make sure that active compounds can fit in your target's binding site. If your experimentally determined target structure was crystallized without a bound ligand, the cavity volume may be insufficient to accommodate active ligands.

In such instances, it is important to induce a new active site conformation that's capable of accommodating active compounds. Induced Fit Docking and MacroModel can both be used to do this.

Induced Fit Docking (IFD) is an easy-to-use and well-validated method for modeling ligand-induced deformation in protein active sites. Beginning with your target structure and a known active compound (perhaps even the endogenous ligand), you can dock the ligand using a flexible receptor model. The IFD interface can be found in the Maestro menu bar under Workflows → Induced Fit Docking.

Please note that IFD calculations use both Glide and Prime. If you do not have access to these programs, you can manually position the ligand in the active site and run a MacroModel minimization and side-chain conformer search. Results will vary depending upon initial ligand placement.

If you do not know what the binding site is, you can use SiteMap to locate potential binding sites.

Keywords: apo, docking, glide, induced fit docking, ifd, active site, crystal, no ligand

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