Getting started with DOCK 3.7: Difference between revisions

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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.
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.
1. [[So you want to set up a lab]]
2. [[Install DOCK 3.7]]


= Timeline =  
= Timeline =  

Revision as of 07:36, 13 March 2014

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.

1. So you want to set up a lab

2. Install DOCK 3.7

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.

Hardware and Operating System

Middleware

Compbio middleware needed to support our software and a computational pharmacology lab.

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 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
build_smiles_ligand top10.smi

If this succeeds without trouble, try a bigger database:

build_smiles_ligand hmdbendo_p0.smi

Test 4. Dock custom library

Go to the directory where you can see working and dockfiles directories from Test 2 above.

setup_db2_lots 1 jobname ~/database/testd # nb directory from Test 3 above.
submit_dock

If you want to submit each db2.gz as a separate job, just use

setup_db2 <db_dir>

where <db_dir> is the directory containing the .db2.gz database files.

Test 5. Run DUD and DUDE benchmarks =

      • NB THIS SECTION IS STILL IN DEVELOPMENT ***

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.