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 atomic charge and desolvation penalty calculations required for database building.
- Omega from OpenEye - for conformation generation required for database building.
- Either PyMol or Chimera for 3D modeling.
- rdkit - recommended but not essential.
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 -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 5. Run the DUD and DUDE benchmarks and generate statistics
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.