pegi3s/hdock-builder repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of HDOCK⁠, a docking software that can be used to predict the binding complexes between two proteins.

⁠Note 1

Because of licensing issues we cannot make available the hdock and createpl executables. Therefore, they must be obtained from here⁠.

After obtaining those files, just put the two executables in a folder and use the following command to create a working docker image called pegi3s/hdock:

docker run --rm -v /var/run/docker.sock:/var/run/docker.sock -v /your/data/dir:/data pegi3s/hdock-builder bash -c "cp /data/* ./ && docker build ./ -t pegi3s/hdock"

⁠Note 2

You just need to do this once, unless you erase the pegi3s/hdock image from your computer in which case you must repeat this step.

In this command, you should replace:

• /your/data/dir to point to the directory that contains the hdock and createpl executables.

⁠Using the HDOCK image in Linux

Once the pegi3s/hdock image is created, you can use the following command to run a local instance of the software:

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/hdock bash -c "/exe/hdock /data/PDB1.pdb /data/PDB2.pdb -out /exe/Hdock.out && /exe/createpl /exe/Hdock.out /exe/top100.pdb -nmax 100 -complex -models && mkdir -p /data/output && cp *.pdb /data/output"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the PDB files and the list of binding sites residues (optional) you want to use.
• <PDB1.pdb> to the name of the receptor PDB file you want to use.
• <PDB2.pdb> to the name of the ligand PDB file you want to use.
• <output> to the name of the directory under /your/data/dir where the output will be saved. Please note that this variable appears twice in the above command.

For instance, using the PDB files provided as test cases, together with the hdock and createpl executables, you should run:

docker run --rm -v /your/data/dir:/data pegi3s/hdock bash -c "/exe/hdock /data/1CGI_r_b.pdb /data/1CGI_l_b.pdb -out /exe/Hdock.out && /exe/createpl /exe/Hdock.out /exe/top100.pdb -nmax 100 -complex -models && mkdir -p /data/output && cp *.pdb /data/output"

In this command, if you only change the /your/data/dir, the results will be saved on a folder named output under /your/data/dir.

To see the HDOCK help, just run: docker run --rm pegi3s/hdock bash -c "/exe/hdock -help".

⁠Using the HDOCK image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

In order to create the HDOCK image, you should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data -v /var/run/docker.sock:/var/run/docker.sock pegi3s/hdock-builder bash -c "cp /data/* ./ && docker build ./ -t pegi3s/hdock"

and then run: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/hdock bash -c "/exe/hdock /data/PDB1.pdb /data/PDB2.pdb -out /exe/Hdock.out && /exe/createpl /exe/Hdock.out /exe/top100.pdb -nmax 100 -complex -models && mkdir -p /data/output && cp *.pdb /data/output"