DOCK6 POSE Reproduction

The purpose of this tutorial is to provide people with instructions on how to perform a commonly used test, pose reproduction that evaluates DOCK6's ability to reproduce known experimental results.

I. Introduction

     DOCK6 is a commonly used docking protocol which assess the affinity of a ligand, a drug candidate to a target site (Protein, Enzyme, RNA). To evaluate a software's ability to accurately reproduce experimental results, an experiment called Pose Reproduction. 

     Pose Reproduction used an experimental known ligand and protein complex from the PDB database and attempts to dock this ligand back into it's original location. If the lowest energy ligand(most energetically favorable) is within 2.0 RMSDh of the original target site, this is referred to as a docking success. If any of the ligands, but not the lowest energy ligand is within 2.0 RMSDh of the original target site, this is referred to as a scoring failure. If none of the ligands are within 2.0 RMSDh of the original target site this is referred to as a sampling failure. 

II. Preparing DOCK directories

     The first step in this process is to prepare all of the DOCK6 directories for each of the systems present. The first step in the procedure is to prepare all a directory for each PDB system. The testset used in this docking protocol was the SB2012 test set with 1043 systems. The testset should be formatted as below with a separate directory for each PDB system.

PDB Directories

~121P/ 181L/ 182L/ 183L/ 184L/ etc/

     Following this