Difference between revisions of "Tutorial on running DOCK3.7 with GIST"

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# use the align the receptor and ligand to the MD frame.
 
# use the align the receptor and ligand to the MD frame.
 
 
# prepare the receptor for docking using blastermaster.  Flexible receptor docking is approximated by docking to 16 states.   
 
# prepare the receptor for docking using blastermaster.  Flexible receptor docking is approximated by docking to 16 states.   
 
 
# modify the INDOCK file.
 
# modify the INDOCK file.
 
 
# download (or generate) ligand and decoy DUD-E like databases.  
 
# download (or generate) ligand and decoy DUD-E like databases.  
 
 
# Dock ligand and decoy databases and perform enrichment analysis
 
# Dock ligand and decoy databases and perform enrichment analysis
 
 
# perform enrichment analyis
 
# perform enrichment analyis

Revision as of 09:35, 30 January 2017

Tutorial by Trent Balius (2017/01/30).

This tutorial assumes that you have already completed the MD tutorial [Tutorial on running Molecular Dynamics for GIST grid generation].

  1. use the align the receptor and ligand to the MD frame.
  2. prepare the receptor for docking using blastermaster. Flexible receptor docking is approximated by docking to 16 states.
  3. modify the INDOCK file.
  4. download (or generate) ligand and decoy DUD-E like databases.
  5. Dock ligand and decoy databases and perform enrichment analysis
  6. perform enrichment analyis