Getting started with DOCK 3.7: Difference between revisions

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= Test 1: Basic tests =  
= 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.
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 $DOCKBASE/test
  cd ~/$DOCKBASE/test
  ./all-test.sh
  ./all-test.sh
This should run about 10-30 minutes depending on your hardware, and should either produce clear error messages (work needed) or a clear message that the tests succeeded without problems. 


= Test 2: 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.
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/
Line 54: Line 54:
= Test 3. Prepare library for docking =
= Test 3. 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
dbgen.csh top10.smi
If this succeeds without trouble, try a bigger database:
dbgen.csh hmdbendo_p0.smi


= Test 4. Dock custom library =  
= Test 4. Dock custom library =  
* get library in right place
* set up docking in Test 2 above to dock the libraries created in Test 3 above.
* dock
* step by step instructions.


= Test 5. Run the DUD and DUDE benchmarks and generate statistics =  
= Test 5. Run the DUD and DUDE benchmarks and generate statistics to assess how well docking is working =  
* [[Download DUD]]
* [[Dock DUD]]
* [[Run analysis tools on DUD]]
 
* [[Download DUDE]]
* [[Dock DUDE]]
* [[Run analysis tools on DUDE]]


= Test 6. Acquire public library and dock it =  
= Test 6. Acquire public library and dock it =  
[[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).  
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 =
= Test 7. Dock starting from PDB code =
* run be_blasti
* [[Run be_blasti]]
* run blastermaster
* run blastermaster (see Test 2 above)
* run docking
* run docking (see test 4 above)


= Test 8. Perform fine-tuned docking run =
== fine tune docking spheres (hot spots) ==
* step 1
* step 2
* step 3


= Test 8. Perform fine-tuned docking run =
== fine tune VDW spheres ==
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
== fine tune bounding box ==
* a zinc ion and its coordinating residues
* 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]].
Return to [[DOCK 3.7]].

Revision as of 23:18, 24 February 2014

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!

Acquire 3rd party software

  • rdkit - recommended but currently not essential for the DOCK 3.7 pipeline.
  • 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. 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

This should run about 10-30 minutes depending on your hardware, and should either produce clear error messages (work needed) or a clear message that the tests succeeded without problems.

Test 2: 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

Test 3. 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
dbgen.csh top10.smi

If this succeeds without trouble, try a bigger database:

dbgen.csh hmdbendo_p0.smi

Test 4. Dock custom library

  • set up docking in Test 2 above to dock the libraries created in Test 3 above.
  • step by step instructions.

Test 5. Run the DUD and DUDE benchmarks and generate statistics to assess how well docking is working

Test 6. 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).

Test 7. Dock starting from PDB code

  • Run be_blasti
  • run blastermaster (see Test 2 above)
  • run docking (see test 4 above)

Test 8. 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.