What is the difference between Strain Rescore (in the Script Center) and Emodel?

Emodel is Glide's internal score for ranking poses. It includes Einternal, and a greater weighting of the force field (i.e.,Coulomb-vdW) energies, so it is well-suited for selecting the top poses of a particular ligand, but not as suitable for comparing chemically distinct structures. For comparing poses of different ligands, the GlideScore is used.

The Strain Rescore script performs the same type of calculation as the "Apply strain correction terms" option on the Output tab of the Glide Ligand Docking panel, but it does so with MacroModel as the post-processing application. Because Glide docking involves fitting ligands into a fixed receptor structure with scaled vdW radii, some ligand strain is allowed in order to compensate for the lack of receptor flexibility. However, it is difficult to tell whether ligand strain is an artifact of the docking method, or an indication of a false positive (i.e., strain the would persist even if the complex were allowed to relax). Therefore we developed the strain correction as a way to identify ligands with too much strain: ligands with more than 4 kcal/mol energy difference (by default) between the docked and free conformations receive penalties.

This protocol was developed prior to the addition of post-docking minimization, which generates less strained ligand conformations, and therefore has greatly reduced the need for such strain corrections. However, even with post-docking minimization, Glide can sometimes produce strained ligand poses, so you might find it useful in some situations.

Keywords: Strain Rescore, Emodel, GlideScore, strain correction, Glide

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