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]].


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 =
= 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.
  mkdir -p ~/docking/test1
  mkdir -p ~/docking/test1
Line 11: Line 11:
  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 22: Line 22:
  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 31: Line 31:
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 44: Line 44:
* [[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

Revision as of 08:22, 13 March 2014

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.