Article ID: 56 - Last Modified: June 7, 2011
In a Glide docking study, I requested 15 poses but I received feedback that the degeneracy check includes only 10 poses. Is Glide checking all of the poses in the output or is the number of checked poses internally limited?
Glide will not necessarily return as many poses as you've requested. When setting up a Glide docking job, the specified number of poses to return is simply an upper bound on the number of poses returned per ligand. Glide searches for good, distinct poses, not an arbitrary number of poses. Thus, if Glide finds fewer good, distinct poses than the number of poses requested, only those good, distinct poses are reported. This is particularly true for Glide XP, because poses are passed to final scoring only if they are within a certain Emodel window of the top pose.
In summary, the number of poses is internally limited by (1) Glide's consideration of what poses are good enough to survive its various filters, and (2) Glide XP's Emodel window. The number of poses returned will depend greatly on the receptor. For a tight active site, only a few poses may be returned whereas, for most systems, Glide SP will generally return the number of poses requested during set-up of the job. For Induced Fit Docking, 20 poses per ligand are requested by default and 20 poses are typically returned.
Keywords: Glide, poses, maximum
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