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In my Glide docking results I am seeing multiple very similar poses for a given ligand. I thought Glide was supposed to eliminate poses with RMSD less than 0.5 Å or maximum atom displacement less than 1.3 Å, but the poses I am looking at are clearly closer than those cutoff criteria. What is happening here?

Glide has a clustering algorithm that is applied to the final poses in order to only show diverse poses. The default criteria are 0.5 Å RMSD and 1.3 Å maximum atom displacement. However, these settings can be changed in the Advanced Settings dialog in the Output tab of the Glide Docking GUI, so check to see if those settings have been changed.

Another possibility is if you are saving more than 10 poses, the symmetry calculation is turned off. With the symmetry calculation turned off it is possible for symmetric groups to look very similar but produce high RMSD and/or maximum atom displacement values. For Suite 2012, the default number of poses for performing the symmetry checking was increased to 100, and this value can be set with a new keyword, NMAXRMSSYM, in the Glide input file.

A third possibility is that pose elimination was performed prior to post-docking minimization. In some cases, poses that were not considered duplicates before minimization converged to the same structure, resulting in duplicates. In Suite 2012, a test was added to eliminate duplicates after post-docking minimization.

Keywords: Glide, docking, cutoff criteria

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