Article ID: 553 - Last Modified: June 12, 2011
How do I use an ensemble of receptors derived from IFD for virtual ligand screening?
First, use IFD to generate a set of receptor-ligand complexes for your receptor and one or more active ligands, and choose the desired receptor conformations from the results of the IFD run.
For example, the output complexes might have two distinct conformations (A and B) for an active site chain, and certain actives bind when the side chain is in conformation A, while others bind with the side chain in position B. In this case, you would want to include both of these receptor conformations in the ensemble docking.
You can then use the Virtual Screening Workflow to generate the grids for these receptor conformations, and dock a set of ligands to these grids. VSW generates the grids, docks the ligands to each grid, and collates the results in a single job.
Keywords: Glide, IFD, receptor conformations, Virtual Screening Workflow, ensemble docking
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