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Article ID: 695 - Last Modified: May 16, 2011

I need the Emodel energy of the native poses observed in the X-ray structures. With the "score in place" option, however, Glide calculates only the GlideScore values of the input poses, Emodel scores are missing in the output. Can you explain this please?

The Emodel score is calculated for refine-only jobs only if post-docking minimization is performed, but due to the way in which Emodel is calculated, it can't be compared directly to Emodel scores from flexible-docking jobs. There is no pose selection process in a score-in-place job, so Emodel is not calculated. The GlideScore, and components such as the CvdW energy, are calculated for both score-in-place and refinement jobs, however, and can be compared to results from regular flexible-docking jobs.

The details of Emodel are proprietary. Emodel calculation involves not only the specific pose being evaluated, but also other poses found for that ligand. Therefore, it will be different for score-in-place/refine jobs (when it can be calculated at all) than for flexible-docking/rigid jobs, since the latter generate diverse populations of docked poses for each ligand. Emodel scores are used for ranking poses for a given ligand, and are not intended for comparisons between ligands, for which the GlideScore is the appropriate quantity.

It's possible for a pose with a better GlideScore to not be what Glide considers the top pose for that ligand (e.g.,because the better GlideScore is obtained at the cost of increased ligand strain). However, when redocking the native ligand, there shouldn't be much ligand strain, if any, so we would expect the native pose to score well by both GlideScore and Emodel.

Keywords: Emodel, native pose, GlideScore, Glide

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