Article ID: 568 - Last Modified: May 13, 2011
When combining the results from an ensemble docking into one pose viewer file, what is the significance of the GlideScore offset?
The GlideScore does not include any contributions from the internal receptor energy. Therefore, if you're ranking pose docked to different receptor conformations, you might want to shift the GlideScores to account for receptor differences that might otherwise bias a combined ranking for or against a given receptor. In reality, each individual ligand introduces a unique receptor reorganization energy when binding to the receptor. Often, these energy differences are within the noise level of the GlideScore. For some systems, though, the receptor could adopt conformations with significant energy differences (e.g., the DFG-in and DFG-out states of p38 MAP kinase), and it can be useful to shift the GlideScores to account for this.
The challenge is determining appropriate appropriate offsets for your system. If you have experimental binding energies, you could compute offsets for the receptor conformations based on the differences between the computed GlideScores and experimental data.
Another approach would be to look at the average GlideScore for a set of ligands docked to a given receptor, and then use the differences in those averages to adjust the scores for different receptor conformations, on the assumption that higher/lower average GlideScores are compensated by greater/lesser internal receptor strain.
Keywords: GlideScore offset, receptor conformations, Glide
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