How to run and analyze a DOCK run by hand

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Preamble

These step-by-step instructions have been compiled while running the first HEI-docking campaign with DOCK . Hence, they are biased towards the mistakes I made and the specificities of the binding site of the particular protein I was using and are probably far from being complete...

Workflow

The workflow consists of the following steps:

  1. Preparing the protein
  2. Preparing the ligand (if necessary)
  3. Running DOCK
  4. Analysing the results

Acknowledgments

Most of the "wisdom" in this document is based on patient explanations by Michael Mysinger (especially section 3), Johannes Hermann (section 1) and John Irwin. --Kolb 17:48, 9 June 2008 (PDT)