Article ID: 72 - Last Modified: October 24, 2013
In LigPrep, there are options to generate ligand states using either Ionizer or Epik. What is the difference between the two, and how do they affect downstream Glide results?
Ionizer is a utility program that uses very simple rules to predict the protonation states of ligands. Epik uses Hammett and Taft methodology to predict not only ionization states, but also the energetic penalties associated with them. Epik can also predict different tautomeric forms and calculates energetic penalties for every ligand state it predicts.
Glide can calculate a compound's Docking Score by adding the Epik state penalty to the compound's GlideScore. Docking Score is about 30% better than GlideScore at separating active compounds from inactive compounds. The use of Epik thus improves the enrichment over the use of Ionizer because of the improved scoring.
Ionizer is a free utility included with all Schrodinger software downloads, and Epik requires a license to run.
Keywords: tautomer, tautomerization, GlideScore, DockingScore, enrichment
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