Autodock Crankpep (ADCP) is an in silico peptide docking engine for the popular AutodockFR suite. ADFR is somewhat deprecated and difficult to install on modern systems, not least because it isn't Python 3 compatible, but remains a very useful, open and scalable tool for in silico peptide screening. This repository contains the necessary files that I used to build a Docker container which contains a fully working implementation of ADFR.
The container itself can be pulled from Dockerhub at https://hub.docker.com/r/simonbushell/adfr_docker
This container can be run interactively using data files on mounted volumes. To mount the current directory and run the container:
Mac OS and *nix systems
docker run -it -v $(PWD):/data simonbushell/adfr_docker:v1.0 bash
Windows Powershell
docker run -it -v ${PWD}:/data simonbushell/adfr_docker:v1.0 bash
Windows Cmd.exe
docker run -it -v %cd%:/data simonbushell/adfr_docker:v1.0 bash
This will open up an interactive bash shell within the container with your current directory mounted at /data. The container also contains the ADCP tutorial files at /ADCP_tutorial_data
This repository also contains a docker-compose file where the volume can be stated explicitly. Edit the docker-compose.yml to include your desired volume (ie. under volumes). Run the following comand in the same directory as the docker-compose.yml file
docker-compose run --service-ports myapp bash
If you wish to build your own copy of this container, run the following in the same directory as the Dockerfile. This directory will also need to contain a zip copy of the tutorial files (ADCP_tutorial_data.zip), and the tmpinstall.dat file, to build properly. You will also need a copy of the Linux ADFR tarbell
docker build -t your-image-name .
tmpinstall.dat is a modified form of the install.py file for ADFR. It removes the prompt that asks the user to choose between the academic or commercial version of ADFR (some components of ADFR require a licence for commerical use). This prompt can cause issues duing the container build process and so this modified file will default to the academic version (which contains the MSMS component for molecular surface calculation) as default. Please ensure you obtain a licence if you are using in a commercial setting.