Difference between revisions of "DOCK 3.7 tutorial based on Webinar 2017/06/28"

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  wget https://files.rcsb.org/download/1M17.pdb --no-check-certificate
  wget https://files.rcsb.org/download/1M17.pdb --no-check-certificate
[[File:DOCK3.7tuturial.2017.06.28.2.png|thumb|center|500px|Break Xtal into Receptor and Ligand Files

Revision as of 13:14, 28 June 2017

Scenario 1: Use docking to predicted how Erlotinib (an approved drug) binds to the Epidermal Growth Factor Receptor

Search for Your Molecule in ZINC, Get Files for Docking from ZINC

Get the link from the zinc webpage and us wget to download:

wget http://files.docking.org/protomers/16/89/55/209168955.db2.gz

Put the path of the downloaded database into the split database index file (this file usually contain many db2 file):

ls /path/tutorial_for_webinar/dock3.7/209168955.db2.gz > ligands.sdi

Get the receptor structure from the PDB website

wget https://files.rcsb.org/download/1M17.pdb --no-check-certificate
Break Xtal into Receptor and Ligand Files