Ligand Enrichment Tutorial

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The purpose of this tutorial is to develop a uniform method to test ligand enrichment across the Rizzo lab with the DOCK software.

I.Introduction

     Ligand Enrichment is a common experiment used to evaluate how well a docking program is capable of accurately modeling in vitro experiments. This experiment uses active ligands and decoy ligands to access a docking programs ability to successfully dock to a target site. These active and decoy ligands are roughly the same size and differ due to chemical similarities. These active ligands should bind more favorably(Have a lower energy score) then the decoy ligands if the docking software works properly. 


     The 3 major outcomes for this experiment are early enrichment indicating the active ligands dock more successful in the experiment(The goal for all docking programs), the second is random enrichment indicating that the docking program can differentiate between active and decoy, and late enrichment indicating that docking software gives the lowest energy scores to the decoys which is the worst outcome. The other factor to consider is the degree of early and late enrichment

II.Prepping systems

     The first step is to obtain the active and decoy ligand test set systems which can be found on the Schoichet DUD-E test set website http://dude.docking.org/targets
     Once these targets are obtained unzip these files using the gzip -d actives_final.mol2.gz for the active and gzip -d decoys_final.mol2.gz to decompress files
   
     Prepare the target receptor by either using the official test set ligands or manually prepare a receptor target from scratch