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.)
(This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1.)
Line 21: Line 21:
 
   deactivate
 
   deactivate
  
===making ligand databases.===
+
=== making ligand databases. ===
 
+
get smiles:
+
  
 +
Get smiles:
  
 
for factor Xa it is part of the DUDE database:
 
for factor Xa it is part of the DUDE database:
Line 31: Line 30:
 
   wget http://dude.docking.org/targets/fa10/decoys_final.ism
 
   wget http://dude.docking.org/targets/fa10/decoys_final.ism
  
we can download the isomorphic smiles from the dude webpage.   
+
We can download the isomorphic smiles from the dude webpage.   
 +
 
 +
here is a webserver to gerenate decoys.
 +
  [http://dude.docking.org/generate http://dude.docking.org/generate]
  
 
MORE TO COME HERE ON DATABASE PREP...  
 
MORE TO COME HERE ON DATABASE PREP...  
Line 44: Line 46:
 
  bash $DOCKBASE/ligand/generate/build_smiles_ligand.sh ../decoys_final.ism
 
  bash $DOCKBASE/ligand/generate/build_smiles_ligand.sh ../decoys_final.ism
 
  python $DOCKBASE/ligand/finish/db2end-makedata.py decoys
 
  python $DOCKBASE/ligand/finish/db2end-makedata.py decoys
 +
 +
=== Receptor Preparation ===
  
 
==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 13:54, 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

This part of the tutorial uses the GIST development version of DOCK