Article ID: 784 - Last Modified: May 16, 2011
The poses that came out of my Glide docking run did not have a native-like pose. How do I proceed?
In cases like this, it can be useful to run a score-in-place or refine-only job on the native pose. Comparing the GlideScores and Coulomb-VDW energies can provide clues as to whether a scoring or sampling limitation is causing Glide to miss the native binding mode. Another test is to use the native conformation and run in rigid-docking mode.
If the native-like conformations are being generated, but aren't appearing in the final results, you could try widening the funnel (click "Advanced Settings" on the Settings tab).
Keywords: native pose, native-like conformations, Glide
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