Article ID: 933 - Last Modified: May 25, 2011
Does Glide impose a penalty to cis urea ligands? If not, how can I add such a penalty?
No, Glide does not include a penalty for cis urea. This is because experimentation showed that such penalties did not improve enrichment results. However, if you are more concerned with pose-prediction than enrichment, then applying a geometric penalty for cis urea to the GlideScore could be beneficial.
There isn't any way to do this within Glide itself, so you'd have to do it in a post-processing step. If you do so, you should generate multiple poses per ligand during docking, so that your adjusted GlideScores can be used to select the best pose of the urea compounds (rather than simply penalize urea compounds for which Glide picked cis as the top pose).
Keywords: Glide, cis urea, penalty
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