This is the docker version of the XRRpred: predictor of resolution and r-free in protein X-ray crystallography
You only need docker, access to dockerhub, and the files in this repository to run the tool. It is tested on Ubuntu 20.04.2 LTS (and docker version detailed in docker_version.txt), but it should work on any docker implementation.
If you prefer to install XRRpred directly on your machine or you want to retrain the models, you should use the other repository, which requires you to set up the dependencies like iupred, asaquick. However for using the tool for prediction, it is strongly recommended to use the docker approach explained here.
after cloning (or downloading and extracting) the repository, the next step is to build the image by entering the following command in the root folder of the repository:
docker build -t xrrpred docker_context -f XRRpred.dockerfile
This creates a docker image named xrrpred.
To run XRRpred on an input fasta, you should enter the following command (including < and > characters):
docker run -i xrrpred XRRpred/dockerinout < example.fasta > results.tar.gz
example.fasta is the path to input file and results.tar.gz is the path to output file.
Input fasta file should be formatted like the file example.fasta included in the repostiory. The format is also explained below.
XRRPred accepts one or more proteins as input. The input protein sequences should be in the FASTA format, where for the multiple-chain proteins the chain sequences must use the same prefix in their ID (before the underscore). Example below shows the formatting for two proteins where proteinID1 has two chains (chainID1 and chainID2) and proteinID2 has one chain.
>proteinID1_chainID1
AMINOACIDSEQUENCE
>proteinID1_chainID2
AMINOACIDSEQUENCE
>proteinID2
AMINOACIDSEQUENCE
you can also look at the example file example.fasta
the output is produced in a tar archive including the csv resutls and the visualizations. you can find an example output included in the repository (example_results.tar.gz)