pegi3s/whiscy
WHISCY (http://milou.science.uu.nl/services/WHISCY/) docker image.
110
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.
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
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 pegi3s/whiscy