How can I compare covalent docking results for multiple ligands?

Covalent docking 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.

It may be possible to use Glide to rank the ligands as described in Article 1648

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 Script Center on our web site) and compare between the different poses. Note that this script requires Canvas.

Keywords: covalent docking, Prime, scoring, rank ordering

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

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