Article ID: 671 - Last Modified: May 3, 2011
How can I cluster ligand poses generated by Glide, within a root-mean-square-deviation of 2.0Å?
Glide itself doesn't do this kind of clustering (unless you are referring to increasing the duplicate pose elimination criterion to 2.0 Å). However, we have several scripts on our website (Resources & Downloads → Script Center) that do clustering.
The one that might work for you is the 'pose_entropy.py' script (in the Docking section), which clusters Glide results by ligand in order to compute a modified GlideScore using the number of poses in each energy well. Another script that is intended for clustering of conformers is conformer_cluster.py. This script could be used to cluster the poses of a single ligand by geometric distance.
Keywords: clustering, pose_entropy.py, script
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