PracticalDocking
From I571/ChE531 2007 Class Wiki
Here we will be converting some 2D structures to 3D using OMEGA, docking them into the 1YC4 protein with FRED, and then visualizing the results with VIDA or JMOL.
For these experiments, we will be using the mrtd50.smi, a 50-compound subset of the mrtd.smi dataset, taken from the FDA's Maximum Recommended Therapeutic Dose page. The runs will be done on the cheminfo.informatics.indiana.edu machine.
Set up environment
mkdir docking cd docking cp /var/www/html/djwild/mrtd100.smi . echo $OE_DIR
if not set
OE_DIR=/usr/local/openeye
Generate 3D conformers from 2D SMILES structures
$OE_DIR/bin/omega2 --help simple $OE_DIR/bin/omega2 -in mrtd50.smi -out mrtd50.mol2 -maxconfs 20 -fraglib $OE_DIR/data/omega2/fraglib.oeb.gz
Get 1YC4 protein and box file
cp /var/www/html/djwild/1YC4.pdb . cp /var/www/html/djwild/fred_box.mol2 .
Dock 3D structures into the protein
$OE_DIR/bin/fred --help all $OE_DIR/bin/fred -pro 1YC4.pdb -box fred_box.mol2 -dbase mrtd50.mol2 -oformat mol2
Visualize the structures and scores - chemgauss3_docked.mol2 - chemgauss3_scores.txt