Article ID: 794 - Last Modified: December 4, 2010
Can you tell me about the 'sa' and 'ln' ligand efficiency metrics?
We developed the sa (surface area) and ln (natural log) scalings of the ligand efficiency to better fit the experimental data for maximal affinity of ligands, as in Kuntz et al., PNAS 1998:
The idea for the sa metric is that the affinity more likely scales with the surface area of the molecule that can make interactions with the protein as opposed to the volume, which is what the number of heavy atoms is essentially measuring. The ln metric has no real physical grounds but seems to be a good fit to the Kuntz data.
Keywords: Glide, ligand efficiency
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