Getting started with DOCK 3.7

You want to install the DOCK 3.7 package on your own system, including the entire docking pipeline and database building. These are the notes I made while doing it. Just recommendations. You are free to simply download the software and experiment!

Acquire 3rd party software

• Recommend Centos 6.3 or higher, but other unixes should work
• python 2.7 series - We do not support the 3.x series, and 2.5 or earlier can also cause problems.
• AMSOL - for database building
• omega from OpenEye - for database building
• you need either PyMol or [chimera. Chimera is free to academics and cheap for companies and is ready to use immediately. PyMol is cheap for academics, and there is a free version, but it is some work to get going.

Acquire our software

Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html. Request DOCK 3.7.

cd
mkdir code
cd code
cp ~xyz/DOCK.tgz . # or get distro from dock.compbio.ucsf.edu website as above
tar xzf DOCK.tgz  # unpack

set up .cshrc (or .bashrc equivalent)

You need to create something like this, depending on your exact circumstances.

setenv DOCKBASE /raid4/people/mattchu/code/DOCK
setenv SOFT /raid3/software
setenv ENV_PYTHON "$SOFT/python/bin/python-env.csh 2.7"
source $ENV_PYTHON
set path = ($path $DOCKBASE/bin)
setenv AMSOLEXE $DOCKBASE/bin
setenv OE_DIR /raid3/software/openeye/current
alias pymol ~/pymol/pymol
if ( $?PYTHONPATH ) then
   if ( `echo $PYTHONPATH | grep -c 'openeye/python'` == 0 ) then
       setenv PYTHONPATH $OE_DIR/python:${PYTHONPATH}
   endif
else
   setenv PYTHONPATH $OE_DIR/python
endif

Test 1: Basic tests

This will tell you quick what you forgot to install or if there is any obvious problem with your installation. If you can pass the tests, you are ready to proceed to the following steps.

cd $DOCKBASE/test
./all-test.sh

Test 2: Docking preparation from receptor and ligand alone

Here we prepare the endogenous human metabolites for docking.

cd
mkdir -p docking/test1
cd $DOCKBASE/test/data/xiap/proteins/initial
cp rec.pdb xtal-lig.pdb ~/docking/test1/
cd ~/docking/test1/
blastermaster.py -v

Test 3. Prepare library for docking

Here we prepare the endogenous human metabolites.

cd
mkdir -p database/testa
cd database/testa
wget http://zinc.docking.org/db/byvendor/hmdbendo/hmdbendo_p0.smi.gz
gunzip hmdbendo_p0.smi.gz
*dbgen.csh

Test 4. Dock custom library

• get library in right place
• dock

Test 6. Acquire public library and dock it

DOCK 3.7 uses a format new to this version of DOCK called [mol2db2 format]]. It will be available via the normal channels in ZINC. You can of course also prepare your own version locally. As of this writing, you can currently get pre-prepared subsets of lead-like and fragment-like from our server (details to go here).

Test 7. Dock starting from PDB code

• run be_blasti
• run blastermaster
• run docking

Test 8. Perform fine-tuned docking run

In this docking run, we are going to make adjustments from the default protocol in several areas:

• the docking spheres or hot-spots
• the vdw grids
• the electrostatics grids
• the size of the box
• a zinc ion and its coordinating residues

Return to DOCK 3.7.