Article ID: 604 - Last Modified: December 4, 2010
Can you provide some details on how the strain energy is used?
The normal 'strain energy' incorporated into Emodel is just the Einternal term, which is a local strain computed with a truncated version of OPLS that includes only torsions and 1,4 vdW interactions.
Longer-range interactions are ignored in order not to penalize close intra-ligand contacts that form when fitting the ligand into the rigid-receptor active site.
The strain corrections computed when you select "Apply strain correction terms" (on the Output tab) are determined by:
1. Minimizing the ligand with tight harmonic restraints (E_bound)
2. Minimizing the ligand with soft harmonic restraints (E_unbound)
3. Computing the difference dE = E_bound - E_unbound
4. Applying a correction dE to Emodel and a correction E_corr = 0.25*(dE - 4.0) to GlideScore if E_corr > 0.0.
The 0.25 and 4.0 factors were selected after extensive testing with Glide's enrichment suite. However, this work was done prior to the addition of post-docking minimization (PDM). Since PDM reduces much of the ligand strain observed in previous Glide results, it's possible that a readjustment of these parameters (i.e., smaller cutoff and/or larger scaling factor) could improve the feature's effectiveness. You can adjust these factors in the Advanced Options dialog box of the Output tab.
Keywords: Glide, strain energy
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