Article ID: 563 - Last Modified: May 13, 2011
Is it possible to score an interaction between protein and ligand given by other software (e. g., a MacroModel optimised structure) using the Glide scoring function?
Yes, it is possible to obtain protein-ligand interactions using the Glide scoring function on an already optimized structure. For this, you would have to select the 'Score in place (do not dock)' option in the Settings tab of the Ligand Docking panel of Glide.
This option uses the input coordinates to position the ligand for scoring. Therefore, it requires accurate initial placement of the ligand with respect to the receptor.
Also we advise you to not to use Glide XP with this option since a full XP sampling is normally needed to avoid strong XP penalties for ligands that should be able to dock correctly.
Keywords: GlideScore, protein-ligand interactions, Ligand docking, score in place, Glide
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