View source for Getting started with DOCK 3.7

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]].

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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.
* 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 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]].


[[Category:DOCK 3.7]]
[[Category:Internal]]
[[Category:Tutorials]]
[[Category:NEED ATTENTION]]