View source for Getting started with DOCK 3.7

Here are steps to get [[DOCK 3.7]] installed and running on your own system, including the entire docking pipeline and database building.

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= Acquire 3rd party software =
== Essential ==
* Computer and operating system. We recommend [[Centos]] on either Intel or AMD. We use Centos 6.3, but many other unixes should work. [[Supported platforms for DOCK 3.7]].
* [[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.
* [[Matplotlib]] - currently only needed for analysis plots (enrichment)
* [[MSMS]] - currently only needed by [[be_blasti]]

* [[rdkit]] - recommended but currently not essential for the DOCK 3.7 pipeline.
* [[OGS/GE]] - queuing system.  OpenGridEngine is included in [[Centos]] and you do not need to install it separately.

= 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 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
 set path = ($path $DOCKBASE/bin)
 setenv AMSOLEXE $DOCKBASE/bin/amsol-mod4
 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
This should run about 10-30 minutes depending on your hardware, and should either produce clear error messages (work needed) or a clear message that the tests succeeded without problems.  

= Test 2: Docking preparation from receptor and ligand alone =
Here we prepare the endogenous human metabolites for docking.
 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.
 mkdir -p ~/database/testa
 cd ~/database/testa
 wget http://zinc.docking.org/db/byvendor/hmdbendo/hmdbendo_p0.smi.gz
 gunzip hmdbendo_p0.smi.gz
 head hmdbendo_p0.smi > top10.smi
 dbgen.csh top10.smi
If this succeeds without trouble, try a bigger database:
 dbgen.csh hmdbendo_p0.smi

= Test 4. Dock custom library = 
* set up docking in Test 2 above to dock the libraries created in Test 3 above.
* step by step instructions.

= Test 5. Run the DUD and DUDE benchmarks and generate statistics to assess how well docking is working = 
* [[Download DUD]]
* [[Dock DUD]]
* [[Run analysis tools on DUD]]

* [[Download DUDE]]
* [[Dock DUDE]]
* [[Run analysis tools on DUDE]]

= Test 6. Acquire public library and dock it = 
Use [[ZINC Subset DB2 file locations]] to locate [[mol2db2 format]] libraries of popular subsets until they are available in [[ZINC]] (later in 2014).

= Test 7. Dock starting from PDB code =
* [[Run be_blasti]]
* run blastermaster (see Test 2 above)
* run docking (see test 4 above)

= Test 8. Perform fine-tuned docking run =
== fine tune docking spheres (hot spots) ==
* step 1
* step 2
* step 3

== fine tune VDW spheres ==
* step 1
* step 2
* step 3

== fine tune bounding box ==
* step 1
* step 2
* step 3

== handle ZINC ion and its coordinating residues ==
* step 1
* step 2
* step 3

== fine tune electostatics (tarting up) ==
* step 1
* step 2
* step 3

== fine tune other features of docking (enumerate) ==
* one
* two
* three

Return to [[DOCK 3.7]].


[[Category:DOCK 3.7]]
[[Category:Internal]]
[[Category:Tutorial]]