138 A Practical Guide to Cancer Systems Biology
III. Load the protein structure file into a molecular editor (e.g., PyMol)
and remove any water molecules in it. Remove any other things you
don’t need in this process.Do not close your molecular editor yet! We need it in the next step.To accomplish such task with PyMol, you may need the following
commands:select,remove,andsave.
For all possible commands usable in PyMol, along with detailed
description about how to use those commands, please navigate
to PyMol wiki here: http://www.pymolwiki.org/index.php/Category:
Commands.
IV. Check the dimension of binding site box of your protein in your
molecular editor and take note about it.
In essence, you should take note ofcenterandsizeof the binding site
box.
In PyMol, you may useselectcommand to pick the native ligand
(i.e., the ligand comes with the protein crystal) or amino acid residues
near the binding site, then usegetextentcommand to get dimensions
of this box.
V. Use the following command to prepare protein structure in your shell
prompt:
cat protein.pdb |obabel -ipdb --AddPolarH -xr -xc
-opdbqt > proteino.pdbqt
or
obabel -ipdb protein.pdb --AddPolarH -xr -xc -opdbqt
-Oproteino.pdbqt
VI. Edit producedproteino.pdbqtfile, then save asprotein.pdbqt:
Retain lines starting withATOMtag and remove all others.
You may use application grep for this task if you are using
GNU/Linux, Cygwin or MinGW:
grep ATOM proteino.pdbqt > protein.pdbqt
VII. Write the configuration file for docking like the following:
receptor = protein.pdbqt
ligand = ligand.pdbqt
out = output.pdbqt
centerx = 2.5
centery = 2.5