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, analysis tools and database building.
Timeline
Once you have all the software and hardware, you can get up and running at a basic level in less than a day. If you do not have all the software, plan for a few days of work. If you've never had your own molecular docking lab, plan for at least a week to learn the basics (and a lifetime to master). Once you have a basic installation running, plan for a few days to get a queuing system working the way you like it. We may be able to help. Ask us, but please read this wiki first.
Acquire 3rd party software
Essential
- Computer and operating system. We recommend Centos on either Intel or AMD. Supported platforms for DOCK 3.7.
- Python - 2.7 series
- AMSOL - atomic charge and desolvation penalty calculations required for database building.
- Omega by OpenEye - conformation generation required for database building.
- 3D modeling - PyMol or Chimera
- Matplotlib - currently only needed for analysis plots (enrichment)
- MSMS - currently only needed by be_blasti
Recommended
- rdkit - recommended and soon to be 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.
mkdir -p ~/code/DOCK cd ~/code/DOCK tar xzf dock3.7.tgz
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 DUD and DUDE benchmarks =
And generate statistics to assess how well docking is working.
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.