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How can I compare covalent docking results for multiple ligands?

In the 2013-1 release, Schrödinger introduced a new covalent docking protocol that allows for scoring of different ligands, using Glide and Prime MM-GBSA.

In earlier releases, the covalent docking protocol identifies the lowest-energy poses for each ligand, but although energy-based ranking works well for conformers of the same ligand, it is not suitable for comparison of poses of chemically distinct ligands.

You may also want to look at how the different ligands interact with active site residues, using a script like Interaction Fingerprints (available under Cheminformatics on the Scripts menu in Maestro) and compare between the different poses. Note that this script requires Canvas.

Keywords: rank ordering

Related Articles:

#1648: Can I use Glide to score poses produced by Prime Covalent Docking?

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