dock2interaction_profile

This is a simple script to use plip to batch analysis of interactions between proteins and ligands that are results of smina (vina) docking.

Note that you should change the directory settings in the script, you can also change the process number in the script.

The script can combine the ligands and receptors automatically, just prepare the receptor directory and results directory.

dependence

plip
openbabel

how to obtain plip:

docker pull pharmai/plip:latest

Usage

Your work directory should look like this:

.
├── analysis.sh
├── dock2interaction_profile.md
├── receptor
│   ├── receptor1
│   │   ├── A0A1D8AVC9.pdb
│   │   ├── A0A1D8AVC9_addH.pdbqt
│   │   └── A0A1D8AVC9_fix.pdb
│   └── receptor2
│       ├── A0A1J5S7S8.pdb
│       ├── A0A1J5S7S8_addH.pdb
│       ├── A0A1J5S7S8_addH.pdbqt
│       └── A0A1J5S7S8_fix.pdb
└── results
    ├── receptor1_ligand1
    │   ├── receptor1_ligand1.pdbqt
    │   ├── receptor1_ligand1_01.pdbqt
    │   ├── receptor1_ligand1_02.pdbqt
    │   ├── receptor1_ligand1_03.pdbqt
    │   ├── receptor1_ligand1_04.pdbqt
    │   ├── receptor1_ligand1_05.pdbqt
    │   ├── receptor1_ligand1_06.pdbqt
    │   ├── receptor1_ligand1_07.pdbqt
    │   ├── receptor1_ligand1_08.pdbqt
    │   ├── receptor1_ligand1_09.pdbqt
    │   ├── receptor1_ligand1_10.pdbqt
    │   ├── receptor1_ligand1_11.pdbqt
    │   ├── receptor1_ligand1_12.pdbqt
    │   ├── receptor1_ligand1_13.pdbqt
    │   ├── receptor1_ligand1_14.pdbqt
    │   ├── receptor1_ligand1_15.pdbqt
    │   ├── receptor1_ligand1_16.pdbqt
    │   ├── receptor1_ligand1_17.pdbqt
    │   ├── receptor1_ligand1_18.pdbqt
    │   ├── receptor1_ligand1_19.pdbqt
    │   ├── receptor1_ligand1_20.pdbqt
    │   ├── receptor1_ligand1_21.pdbqt
    │   ├── receptor1_ligand1_22.pdbqt
    │   ├── receptor1_ligand1_23.pdbqt
    │   ├── receptor1_ligand1_24.pdbqt
    │   ├── receptor1_ligand1_25.pdbqt
    │   ├── receptor1_ligand1_26.pdbqt
    │   ├── receptor1_ligand1_27.pdbqt
    │   ├── receptor1_ligand1_28.pdbqt
    │   ├── receptor1_ligand1_29.pdbqt
    │   ├── receptor1_ligand1_30.pdbqt
    │   ├── receptor1_ligand1_31.pdbqt
    │   ├── receptor1_ligand1_32.pdbqt
    │   ├── receptor1_ligand1_33.pdbqt
    │   ├── receptor1_ligand1_34.pdbqt
    │   ├── receptor1_ligand1_35.pdbqt
    │   ├── receptor1_ligand1_36.pdbqt
    │   ├── receptor1_ligand1_37.pdbqt
    │   ├── receptor1_ligand1_38.pdbqt
    │   ├── receptor1_ligand1_39.pdbqt
    │   └── receptor1_ligand1_40.pdbqt
    └── receptor2_ligand1
        ├── receptor1_ligand11.pdbqt
        ├── receptor1_ligand1_01.pdbqt
        ├── receptor1_ligand1_02.pdbqt
        ├── receptor1_ligand1_03.pdbqt
        ├── receptor1_ligand1_04.pdbqt
        ├── receptor1_ligand1_05.pdbqt
        ├── receptor1_ligand1_06.pdbqt
        ├── receptor1_ligand1_07.pdbqt
        ├── receptor1_ligand1_08.pdbqt
        ├── receptor1_ligand1_09.pdbqt
        ├── receptor1_ligand1_10.pdbqt
        ├── receptor1_ligand1_11.pdbqt
        ├── receptor1_ligand1_12.pdbqt
        ├── receptor1_ligand1_13.pdbqt
        ├── receptor1_ligand1_14.pdbqt
        ├── receptor1_ligand1_15.pdbqt
        ├── receptor1_ligand1_16.pdbqt
        ├── receptor1_ligand1_17.pdbqt
        ├── receptor1_ligand1_18.pdbqt
        ├── receptor1_ligand1_19.pdbqt
        ├── receptor1_ligand1_20.pdbqt
        ├── receptor1_ligand1_21.pdbqt
        ├── receptor1_ligand1_22.pdbqt
        ├── receptor1_ligand1_23.pdbqt
        ├── receptor1_ligand1_24.pdbqt
        ├── receptor1_ligand1_25.pdbqt
        ├── receptor1_ligand1_26.pdbqt
        ├── receptor1_ligand1_27.pdbqt
        ├── receptor1_ligand1_28.pdbqt
        ├── receptor1_ligand1_29.pdbqt
        ├── receptor1_ligand1_30.pdbqt
        ├── receptor1_ligand1_31.pdbqt
        ├── receptor1_ligand1_32.pdbqt
        ├── receptor1_ligand1_33.pdbqt
        ├── receptor1_ligand1_34.pdbqt
        ├── receptor1_ligand1_35.pdbqt
        ├── receptor1_ligand1_36.pdbqt
        ├── receptor1_ligand1_37.pdbqt
        ├── receptor1_ligand1_38.pdbqt
        ├── receptor1_ligand1_39.pdbqt
        └── receptor1_ligand1_40.pdbqt

6 directories, 91 files

one command to run analysis:

bash analysis.sh