How to do parameter scanning

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep 
                                                                |
                                                                |------ dockfiles
              |                                                 | 
              |                                                 |----- working
              |                                                 |
              |                                                 ------ rec.pdb, xtal-lig.pdb, INDOCK and other files generated balstermaster.py
              |
              ------- script ------ dockprep_thin_spheres_in_batches.csh
                              |
                              |------ submit_dockprep_thin_spheres.csh
                              |
                              |------ dockprep_thin_spheres.csh
                              |
                              |------ lig-decoy_enrichment.csh
                              |
                              |------ combineScoresAndPoses.csh
                              |
                              |------ AUCplot_of-lig-decoys.csh
                              |
                              |------ mk_matrix_logAUC.py
                              |
                              |------ sph_lib.py
                              |
                              |------ pdb_lib.py
                              |
                              ------- close_sph.py

1) Make those directories above.

mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory

cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.

cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.

cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

  mkdir ligands-decoys
  cd ligands-decoys
  mkdir ligands
  mkdir decoys

now copy your decoys.db2.gz to decoys now copy your ligands.db2.gz to ligands

7) Submit DOCK and enrichment calculation.

csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.

csh /path/to/script/combineScoresAndPoses.csh
csh /path/to/script/AUCplot_of-lig-decoys.csh

9) Visualize the logAUC by heatmap.

python /path/to/script/mk_matrix_logAUC.py