pegi3s/pydock3-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 PyDock3⁠, a software that facilitates the usage of zdock and ftdock protein-protein docking software.

⁠Note 1

Because of licensing issues we cannot make available PyDock3 or zdock files. Therefore, they must be obtained from https://life.bsc.es/pid/pydock/get_pydock.html⁠ and https://zdock.umassmed.edu/software/⁠ respectively.

After obtaining the pyDock3.tgz and zdock3.0.2_linux_x64.tar.gz files, just put it in a empty folder and use the following command to create a working docker image called pegi3s/pydock3:

docker run --rm -v /var/run/docker.sock:/var/run/docker.sock -v /your/data/dir:/data pegi3s/pydock3-builder bash -c "cp /data/* ./ && docker build ./ -t pegi3s/pydock3"

⁠Note 2

You just need to do this once, unless you erase the pegi3s/pydock3 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 pyDock3.tgz and zdock3.0.2_linux_x64.tar.gz files.

⁠Using the PyDock3 image in Linux

Once the pegi3s/pydock3 image is created, you can use the following commands to run zdock, ftdock and several other ftdock utilities:

⁠zdock

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/pydock3 bash -c "./run_zdock project_name number_of_solutions best_PDB restraint"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the PDB and .ini files (see test data for an example of a .ini file).
• project_name to the project name that is the same as the name of the .ini file.
• number_of_solutions to the number of solutions to be analysed (recommended: 100; this number must be smaller or equal to 2000).
• best_PDB to the number of the best solutions to be obtained (recommended: 5).
• restraint to R or r if restrainsts are declared in the .ini file. Any other value if restraints are not declared.

⁠Note 3

In the run_zdock script, zdock is invoked using zdock -o project_name.zdock -R project_name_rec.pdb.H -L project_name_lig.pdb.H and not pyDock3 project_name zdock, because the latter command requires the libg2c.so.0 library that can only be installed in Ubuntu versions older than the oldest one available in DockerHub (Ubuntu 14.04).

⁠ftdock

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/pydock3 bash -c "./run_ftdock project_name number_of_solutions best_PDB restraint"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the PDB and .ini files (see test data for an example of a .ini file).
• project_name to the project name that is the same as the name of the .ini file.
• number_of_solutions to the number of solutions to be analysed (recommended: 100; this number must be smaller or equal to 10000).
• best_PDB to the number of best solutions to be obtained (recommended: 5).
• restraint to R or r if restrainsts are declared in the .ini file. Any other value if restraints are not declared.

⁠Note 4

In the run_ftdock script, ftdock is invoked using ftdock -static project_name_rec.pdb -mobile project_name_lig.pdb > output and not pyDock3 project_name zdock, because the latter command requires the libg2c.so.0 library that can only be installed in Ubuntu versions older than the oldest one available in DockerHub (Ubuntu 14.04).

⁠change chain ID

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/pydock3 bash -c "./run_change_chain_ID PDB old new"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the PDB file to be processed.
• PDB to the PDB file name.
• old to the old chain name.
• new to the new chain name.

⁠Remone non-standard and hydrogen atoms

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/pydock3 bash -c "./run_preprocess PDB"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the PDB file to be processed.
• PDB to the PDB file name.

⁠Optimal Docking Area (ODA) analysis / Interface prediction from protein surface desolvation energy

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/pydock3 bash -c "./run_ODA PDB"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the PDB file to be processed.
• PDB to the PDB file name.

⁠Test data

To test the previous commands, download the test data available here⁠ and then run:

docker run --rm -v /your/data/dir:/data pegi3s/pydock3 bash -c "./run_zdock test 100 5 R"

⁠Using the PyDock3 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 PyDock3 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/pydock3-builder bash -c "cp /data/* ./ && docker build ./ -t pegi3s/pydock3"