Getting started with DOCK 3.7: Difference between revisions

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You want to install [[DOCK 3.7]] on your own system. These are the notes I made while doing it. These are just recommendations, based on my experience. 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:
* Recommend Centos 6.3 or higher, but other unixes should work
* python 2.7 series - We do not support the 3.x series, and 2.6 or earlier can also cause problems.
* amsol - for database building
* omega / OpenEye - for database building


= Acquire our software =
= Docking preparation from receptor and ligand alone =
Here we are installing a private copy under a single user account. It is easy to change 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]].
Here we prepare the endogenous human metabolites for docking.
cd
  mkdir -p ~/docking/test1
  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) =
You need to create something like this, depending on your exact circumstances.
setenv DOCKBASE /raid4/people/mattchu/code/DOCK
setenv SOFT /raid3/software
setenv ENV_PYTHON "$SOFT/python/bin/python-env.csh 2.7"
source $ENV_PYTHON
set path = ($path $DOCKBASE/bin)
 
= Test the installation using the built-in test scripts =
cd $DOCKBASE/test
./all-test.sh
 
= Perform your first docking with pre-prepared files =
cd
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/
  cd ~/docking/test1/
  cd ~/docking/test1/
  blastermaster.py -v
  blastermaster -v


 
= Prepare library for docking =
= Perform your first database generation, using 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]]


= Perform your first docking from PDB code alone using be_blasti =
* All about [[DUDE]]
* run be_blasti
* [[Download DUDE]]
* run blastermaster
* [[Dock DUDE]]
* [[Run analysis tools on DUDE]]


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


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


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


= Get a pre-prepared library =
== handle ZINC ion and its coordinating residues ==
[[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).
* 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]].
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.

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