DOCK 3.7 2014/09/25 FXa Tutorial
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:
If you are using a virtual enviorment for python do something like this:
to leave use the deactivate command:
making ligand databases.
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.
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
DOCK Distribution structure
Here we discuss the directory structure of the distribution, what the different directory contain, and information about the scripts.
Here is the structure:
ls -l ~/DOCK-3.7-beta1.0.1/ total 27 -rw-r--r-- 1 user group 2737 Mar 28 08:43 README.md drwxr-xr-x 2 user group 31 Mar 28 08:43 analysis drwxr-xr-x 2 user group 28 Mar 28 08:43 common drwxr-xr-x 6 user group 7 Mar 28 08:43 docking drwxr-xr-x 3 user group 3 Mar 28 08:43 install drwxr-xr-x 8 user group 9 Mar 28 08:43 ligand drwxr-xr-x 19 user group 19 Mar 28 08:43 proteins drwxr-xr-x 3 user group 15 Mar 28 08:43 test
docking/DOCK contains the dock source code and the the dock binary. docking/submit contains submission scripts to submit jobs to the queue. ligand contains the ligand preparation steps. (this has dependencies not include in the distribution) proteins contains scripts and programs for protein preparations. test contains test to make sure the package is working as intended. Running the tests can help dignose errors and tell you what might be missing.
- Splite your pdb into a rec.pdb and xtal-lig.pdb.
- you can do this by running this script:
The program sphgen will produce spheres that fill the nooks and crannies on the protein surface.
The matching spheres are used during docking to orient the ligand into the binding pocket. The matching spheres are produced by converting the crystallographic ligand atoms into sphere and also using the spheres from sphgen.
This image was made with chimera. To visualize the sphere there should be no sphere with a radius of zero. the recommendation is to change "0.00" to "0.70". Also you should remove the header from the file.
A final important set of spheres are the low dielectric spheres. These spheres are used during the PB calculation to force the binding site to have low dielectric.
This image read shows the spheres in the rec.crg.pdb. This is the file on which qnifft runs the PB calculation.
= pose visualization
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.