Quick start

Simple CaverDock analysis

The most typical basic analysis is very simple and nearly fully automatic. The script uses a single protein structure, one ligand molecule and one pre-computed tunnel geometry. The input files are automatically processed. The input 3D representations of receptor and ligand are converted to PDBQT files needed for the calculation. The tunnel geometry is discretized into a set of discs. CaverDock simulation is executed in the specified direction (binding IN or unbinding OUT) and once it is done, the outputs will be the ligand trajectory and energy profile.

Note

Simple CaverDock analyses can be calculated also using the user-friendly web interface Caver Web.

The only needed inputs for this simple analysis are:

  1. structure of the receptor in the PDB format

  2. structure of the ligand in either PDB or MOL2 format

  3. tunnel from CAVER (for more details see section Tunnel calculation)

Once you have all three files ready, copy them to one directory:

$ mkdir caverdock_analysis
$ cd caverdock_analysis
$ cp /path/to/receptor.pdb /path/to/ligand.pdb /path/to/tunnel.pdb .

And then start the analysis using cd-analysis script:

$ apptainer exec /path/to/caverdock.sif cd-analysis -r receptor.pdb -t tunnel.pdb -l ligand.pdb -d OUT -s LOWERBOUND --keep-bottlenecks

Example CaverDock Analysis data: caverdock_analysis.tar.gz

Once the analysis is finished, you can find all the raw output data (for more details see section CaverDock outputs). Now you can continue to the Results interpretation section to perform results analysis and interpretation.

Simple CaverDock screening

Apart from the basic cd-analysis for single CaverDock calculation we also provide a simple way to perform virtual screening with multiple proteins, tunnels and ligands. To run the screening the user must prepare the necessary structural input files and a yaml file which references all these files to create all possible combinations for the batch calculation. A simple example of such a file is shown below.

receptor_1:
  protein: receptor.pdb
  tunnels:
    - path: tunnel.pdb

ligands_1:
  - ligand.pdb

screenings:
  - name: Simple Screening
    receptors:
      - $ref: receptor_1
    ligands:
      $+:
        - $ref: ligands_1

In this example, the script will run one screening experiment Simple Screening with one protein, one tunnel and one ligand. You can find detailed information about the yaml files and virtual screening with CaverDock API in the section Virtual screening. All receptor-tunnel-ligand combinations will be generated for each defined screening at the start of the screening process.

Once you have everything ready, you can run the screening using cd-screening script:

$ apptainer exec /path/to/caverdock.sif cd-screening -p 4 simple_screening.yaml

Example CaverDock Screening data: caverdock_screening.tar.gz