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 started with [[DOCK 3.7]] . If you don't already have the necessary physical infrastructure, you'll need to [[So you want to set up a lab |set it up]]. If you haven't already installed [[DOCK 3.7]], here are the [[Install DOCK 3.7 | installation instructions]].
 
= 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.


{{TOCright}}
{{TOCright}}


= Acquire 3rd party software =
So, now that you have [[DOCK 3.7]] running, and that basic ./all-test.sh script works, here is how to get started:
== 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 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 =
= Docking preparation from receptor and ligand alone =
Here we prepare the endogenous human metabolites for docking.
Here we prepare the endogenous human metabolites for docking.
  mkdir -p ~/docking/test1
  mkdir -p ~/docking/test1
Line 54: Line 13:
  blastermaster -v
  blastermaster -v


= Test 3. Prepare library for docking =
= Prepare library for docking =
Here we prepare the endogenous human metabolites.
Here we prepare the endogenous human metabolites.
  mkdir -p ~/database/testa
  mkdir -p ~/database/testa
Line 65: Line 24:
  build_smiles_ligand hmdbendo_p0.smi
  build_smiles_ligand hmdbendo_p0.smi


= Test 4. Dock custom library =  
= Dock custom library =  
Go to the directory where you can see working and dockfiles directories from Test 2 above.
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.
  setup_db2_lots 1 jobname ~/database/testd # nb directory from Test 3 above.
Line 74: Line 33:
where <db_dir> is the directory containing the .db2.gz database files.
where <db_dir> is the directory containing the .db2.gz database files.


= Test 5. Run DUD and DUDE benchmarks ==
= Run DUD and DUDE benchmarks ==
***NB THIS SECTION IS STILL IN DEVELOPMENT ***
***NB THIS SECTION IS STILL IN DEVELOPMENT ***
And generate statistics to assess how well docking is working.
And generate statistics to assess how well docking is working.
Line 87: Line 46:
* [[Run analysis tools on DUDE]]
* [[Run analysis tools on DUDE]]


= Test 6. Acquire public library and dock it =  
= 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).
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 =
= Dock starting from PDB code =
* [[Run be_blasti]]
* [[Run be_blasti]]
* run blastermaster (see Test 2 above)
* run blastermaster (see Test 2 above)
* run docking (see test 4 above)
* run docking (see test 4 above)


= Test 8. Perform fine-tuned docking run =
= Perform fine-tuned docking run =
== fine tune docking spheres (hot spots) ==
== fine tune docking spheres (hot spots) ==
* step 1
* step 1
Line 132: Line 91:
[[Category:Internal]]
[[Category:Internal]]
[[Category:Tutorials]]
[[Category:Tutorials]]
[[Category:NEED ATTENTION]]

Latest revision as of 19:03, 10 January 2019

Here are steps to get started with DOCK 3.7 . If you don't already have the necessary physical infrastructure, you'll need to set it up. If you haven't already installed DOCK 3.7, here are the installation instructions.

So, now that you have DOCK 3.7 running, and that basic ./all-test.sh script works, here is how to get started:

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

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

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.

Run DUD and DUDE benchmarks =

      • NB THIS SECTION IS STILL IN DEVELOPMENT ***

And generate statistics to assess how well docking is working.

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).

Dock starting from PDB code

  • Run be_blasti
  • run blastermaster (see Test 2 above)
  • run docking (see test 4 above)

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.

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