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 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.
- 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.