Difference between revisions of "DOCK 3.7 2014/09/25 FXa Tutorial"

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(This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1.)
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[[File:lowdiele.png|thumb|center|375px|1FJS Receptor surface with low dielectric spheres.]]
 
[[File:lowdiele.png|thumb|center|375px|1FJS Receptor surface with low dielectric spheres.]]
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=== pose visualization ==
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use chimera:
  
 
==This part of the tutorial uses the GIST development version of DOCK==
 
==This part of the tutorial uses the GIST development version of DOCK==

Revision as of 17:31, 25 September 2014

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

  1. Splite your pdb into a rec.pdb and xtal-lig.pdb.
    1. you can do this by running this script:

sphgen will produce spheres that file the nooks and crannies.

1FJS Receptor surface with all spheres from sphgen


1FJS Receptor surface with matching spheres

Here is the

1FJS Receptor surface with low dielectric spheres.

= 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.