Open-Omics-Autodock-Vina

Open-Omics-Autodock-Vina is a fast, efficient molecular docking software used to predict ligand-protein binding poses and affinities. It features a refined scoring function, parallel execution on multicore CPUs and user-friendly configuration.

Docker Setup Instructions

1. Build the Docker Image

To build the Docker image with the tag docker_vina, use the following commands based on your machine’s proxy requirements:

For machine without a proxy:
```
docker build -t docker_vina .
```

For machine with a proxy:

docker build --build-arg http_proxy=<http_proxy> --build-arg https_proxy=<https_proxy> --build-arg no_proxy=<no_proxy_ip> -t docker_vina .

2. Choose and Download Protein Complex Data

Select any protein complex from the available dataset of 140 protein-ligand complexes(https://zenodo.org/records/4031961) which you can download from (https://zenodo.org/records/4031961/files/data.zip?download=1). This guide uses the 5wlo protein as an example.

1) Run the below commands to make data download script executable, download the complete dataset and extract the data for 5wlo:

chmod +x data_download_script.sh
bash data_download_script.sh 5wlo

Note: You can replace 5wlo with any other complex name from the complete dataset available in data_original/data directory.

2) Create an output directory to store results specific to 5wlo:

mkdir -p 5wlo_output

3) Set the environment variables for the 5wlo protein as follows:

export INPUT_VINA=$PWD/5wlo
export OUTPUT_VINA=$PWD/5wlo_output

4) Add the necessary permissions to output folder for Docker to write to it:

sudo chmod -R a+w $OUTPUT_VINA

3. Run the Docker Container

Verify that the Docker image was built successfully by listing Docker images:

docker images | grep docker_vina

If the image is listed, run AutoDock Vina with the following command:

docker run -it -v $INPUT_VINA:/input -v $OUTPUT_VINA:/output docker_vina:latest vina --receptor protein.pdbqt --ligand rand-1.pdbqt --out /output/rand-1_out.pdbqt --center_x 16.459 --center_y -19.946 --center_z -5.850 --size_x 18 --size_y 18 --size_z 18 --seed 1234 --exhaustiveness 64

This command will process your receptor and ligand files and place the results in the specified output directory.

4. Expected Output

After running the above command, you should find the output file (rand-1_out.pdbqt) in the output directory, such as 5wlo_output for this example.

The original README content of AutoDock-Vina follows:

AutoDock Vina: Docking and virtual screening program

AutoDock Vina is one of the fastest and most widely used open-source docking engines. It is a turnkey computational docking program that is based on a simple scoring function and rapid gradient-optimization conformational search. It was originally designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab, and it is now being maintained and develop by the Forli Lab at The Scripps Research Institute.

AutoDock4.2 and Vina scoring functions
Support of simultaneous docking of multiple ligands and batch mode for virtual screening
Support of macrocycle molecules
Hydrated docking protocol
Can write and load external AutoDock maps
Python bindings for Python 3

Documentation

The installation instructions, documentation and tutorials can be found on readthedocs.org.