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.

MORE TO COME HERE ON DATABASE PREP...


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

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