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

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MORE TO COME HERE ON DATABASE PREP...  
 
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
  
 
==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 12:20, 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.

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

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