Getting started with DOCK 3.7: Difference between revisions

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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!
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]].


{{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:
* [[Centos]] - we use Centos 6.3 or higher, but many other unixes may 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.
= Docking preparation from receptor and ligand alone =
* [[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
 
= Test 2: 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.
cd
  mkdir -p ~/docking/test1
  mkdir -p docking/test1
  cd $DOCKBASE/test/data/xiap/proteins/initial
  cd $DOCKBASE/test/data/xiap/proteins/initial
  cp rec.pdb xtal-lig.pdb ~/docking/test1/
  cp rec.pdb xtal-lig.pdb ~/docking/test1/
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  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.
cd
  mkdir -p ~/database/testa
  mkdir -p database/testa
  cd ~/database/testa
  cd database/testa
  wget http://zinc.docking.org/db/byvendor/hmdbendo/hmdbendo_p0.smi.gz
  wget http://zinc.docking.org/db/byvendor/hmdbendo/hmdbendo_p0.smi.gz
  gunzip hmdbendo_p0.smi.gz
  gunzip hmdbendo_p0.smi.gz
  *dbgen.csh
  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.
* All about [[DUD]]
* [[Download DUD]]
* [[Dock DUD]]
* [[Run analysis tools on DUD]]
 
* All about [[DUDE]]
* [[Download DUDE]]
* [[Dock DUDE]]
* [[Run analysis tools on DUDE]]


= Test 4. Dock custom library =  
= Acquire public library and dock it =  
* get library in right place
Use [[ZINC Subset DB2 file locations]] to locate [[mol2db2 format]] libraries of popular subsets until they are available in [[ZINC]] (later in 2014).
* dock


= Test 5. Run the DUD and DUDE benchmarks and generate statistics =
= Dock starting from PDB code =
* [[Run be_blasti]]
* run blastermaster (see Test 2 above)
* run docking (see test 4 above)


= Test 6. Acquire public library and dock it =  
= Perform fine-tuned docking run =
[[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).
== fine tune docking spheres (hot spots) ==
* step 1
* step 2
* step 3


= Test 7. Dock starting from PDB code =
== fine tune VDW spheres ==
* run be_blasti
* step 1
* run blastermaster
* step 2
* run docking
* step 3


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


= Test 8. Perform fine-tuned docking run =
== handle ZINC ion and its coordinating residues ==
In this docking run, we are going to make adjustments from the default protocol in several areas:
* step 1
* the docking spheres or hot-spots
* step 2
* the vdw grids
* step 3
* the electrostatics grids
* the size of the box
* a zinc ion and its coordinating residues


== 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]].
Return to [[DOCK 3.7]].
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[[Category:DOCK 3.7]]
[[Category:DOCK 3.7]]
[[Category:Internal]]
[[Category:Internal]]
[[Category:Tutorial]]
[[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.