GlideScore/Docking Score doesn't correlate with my known activities. What is wrong?

Glide is primarily concerned with generating an accurate pose for each ligand and enrichment (the separation of actives from inactives). Extensive testing, both in-house and by 3rd parties has shown that Glide is extremely effective at performing these two tasks.

However, the task of accurately estimating binding for a set of ligands, particularly if they are diverse in structure, remains a very tough problem and an active area of research for Schrödinger.

For simpler cases, where the set of ligands share a common structure for example, there are a couple of related approaches that may yield a more quantitative ranking than the straight Glide or docking scores. The first of these is Prime's MM-GBSA module (which can be found in the Applications menu). This is designed to process output from Glide and can return a estimate of the free energy binding for each of the ligands supplied using a Generalized Born solvation model. The second is Macromodel's Embrace module, which is capable of performing similar calculations to Prime. The Embrace conformation search module however, has the potential to carry out some extremely detailed conformational searches, which while time consuming, may prove crucial to accurate activity estimation.

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