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Article ID: 26 - Last Modified: April 25, 2011

Before running a docking experiment, how can I determine the active site location if my experimental structure doesn't contain a co-crystallized ligand?

You can use SiteMap, which is a program designed to identify and characterize ligand binding sites. In validation studies, the top-scoring cavity identified by SiteMap was the correct binding site in over 90% of all test cases. You can open the SiteMap panel in Maestro with Applications → SiteMap.

Experimental SAR data can help to confirm the validity of SiteMap's predictions.

If you are starting from an apo structure, you may wish to run an Induced Fit Docking (IFD) calculation first, to produce a receptor conformation that is better able to accommodate ligands in (rigid-receptor) Glide docking experiments.

Keywords: SiteMap, Glide, docking, active site, apo

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