pegi3s/whiscy

Sponsored OSS

By i3S

Updated 4 months ago

WHISCY (http://milou.science.uu.nl/services/WHISCY/) docker image.

Image
Data Science
Machine Learning & AI

110

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 WHISCY (WHat Information does Surface Conservation Yield?), a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein.

Using the WHISCY image in Linux

Step 1

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/whiscy whiscy_setup.py /data/input.pdb <chain-protein>

In this command, you should replace:

  • your/data/dir to point to the directory that contains the input PDB file you want to analyze.
  • input.pdb to the actual name of your input PDB file.
  • <chain-protein> to the name of the chain protein you want to use.

For instance, to use chain A of a particular protein, you should run: docker run --rm -v /your/data/dir:/data pegi3s/whiscy whiscy_setup.py /data/input.pdb A

To see the whiscy_setup.py help, just run docker run --rm pegi3s/whiscy whiscy_setup.py --help

Step 2

After chain protein files are generated in Step 1 you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/whiscy whiscy_protocol.sh /data/input_chainprotein

In this command, you should replace:

  • your/data/dir to point to the directory that contains the input chain protein files you want to analyze.
  • input_chainprotein to the actual name of your input file and its chain protein.

For instance, to use chain A files of a particular protein after Step 1, you should run: docker run --rm -v /your/data/dir:/data pegi3s/whiscy whiscy_protocol.sh /data/input_A

Docker Pull Command

docker pull pegi3s/whiscy