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Article ID: 935 - Last Modified:

Is there a way of finding out which of a set of compounds has the core in the same position as the core of my reference compound?

Yes, you can use the Core Constraint and RMSD feature of the Ligand Docking panel. You can set up either a core constraint or just an RMSD calculation with the reference structure. Rather than using the entire reference molecule (or all its heavy atoms) for the calculation, you can specify a substructure SMARTS pattern to define the core, and another pattern for the RMSD.

Keywords: core, Glide, docking

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