DOCK 3.7 2014/09/25 FXa Tutorial
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Written by Trent E Balius and Crystal Nguyen on 2014/09/25
This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1.
see the following for requirements: Install_DOCK_3.7
You must use a version of python (v2.7) that has the follow:
- numpy
- scipy
- matplotlib
- mysql-python
- biopython
If you are using a virtual enviorment for python do something like this:
source /home/tbalius/zzz.virtualenv/virtualenv-1.9.1/myVE/bin/activate.csh
to leave use the deactivate command:
deactivate
making ligand databases.
Get smiles:
for factor Xa it is part of the DUDE database:
wget http://dude.docking.org/targets/fa10/actives_final.ism wget http://dude.docking.org/targets/fa10/decoys_final.ism
We can download the isomorphic smiles from the dude webpage.
here is a webserver to gerenate decoys.
http://dude.docking.org/generate
MORE TO COME HERE ON DATABASE PREP...
Here is what I think is what needs to be done.
mkdir ligands bash $DOCKBASE/ligand/generate/build_smiles_ligand.sh ../actives_final.ism python $DOCKBASE/ligand/finish/db2end-makedata.py ligands
mkdir decoys cd decoys bash $DOCKBASE/ligand/generate/build_smiles_ligand.sh ../decoys_final.ism python $DOCKBASE/ligand/finish/db2end-makedata.py decoys
Receptor Preparation
- Splite your pdb into a rec.pdb and xtal-lig.pdb.
- you can do this by running this script:
sphgen will produce spheres that file the nooks and crannies.
Here is the
= pose visualization
use chimera:
This part of the tutorial uses the GIST development version of DOCK
Put your rec.pdb and xtal-lig.pdb in the same frame as you simulation.
This chimera script might help.