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]].


= Acquire 3rd party software =
{{TOCright}}
* 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 =
So, now that you have [[DOCK 3.7]] running, and that basic ./all-test.sh script works, here is how to get started:
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 deal for companies!) at [http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html]. You want to request [[DOCK 3.7]].
cd
mkdir code
cd code
cp ~xyz/DOCK.tgz . # or get distro from dock website
tar xzf DOCK.tgz  # unpack


= set up .cshrc  (or .bashrc) =
= Docking preparation from receptor and ligand alone =
You need to create something like this, depending on your exact circumstances.
Here we prepare the endogenous human metabolites for docking.
setenv DOCKBASE /raid4/people/mattchu/code/DOCK
  mkdir -p ~/docking/test1
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]]
 
* All about [[DUDE]]
* [[Download DUDE]]
* [[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 docking from PDB code alone using be_blasti =
= 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


= Perform your first fine tuned docking run =
== 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


= Get a pre-prepared library =
== 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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