Docker saves the day – Roadmaps – rivem – Biochemistry Computational Research Facility (BCRF)

rhino b14 roadmap - detail — rhino b14 roadmap – detail

Docker saves the day!

Here is a great example of how Docker can help save a NATURE paper!

Summary:

Problem: Professor wants to use a specific virology program called rivem (links below.) However, this only works on a Linux system.

Solution: download a small, 64Mb, Ubuntu Docker image and run the rivem program inside a Docker container!

This requires just a few steps:

Step 1: download the program: rivem
Step 2: download relevant 3D PDB data, e.g. rhinoviruses B14, A16, and C15 from the Protein Data Bank
Step 3: download the ubuntu docker image from hub.docker.com with command: docker pull ubuntu
Step 4: start the image with a shared directory containing the PDB data, for example:

docker run -it --rm -v $HOME/dockershare/:/data ubuntu

step 5: go to the appropriate directory and run the rivem command to create the roadmap
Step 6: relish in the result!:

rhino b14 roadmap - small — rhino b14 roadmap – small

Links:

rivem is available from Purdue
Missing image of manual at Purdue is visible on this version of the rivem manual from the author now at UTEP

REFERENCES

Xiao C, Rossmann MG, Interpretation of electron density with stereographic roadmap projections. J Struct Biol. 2007 May;158(2):182-7. Epub 2006 Oct 24. PMID:17116403 PMCID:PMC1978246 DOI:10.1016/j.jsb.2006.10.013

Chapman MS, Mapping the surface properties of macromolecules. Protein Sci. 1993 Mar;2(3):459-69.
PMID: 8384042 PMCID:PMC2142375 DOI:10.1002/pro.5560020318

Rossmann MG, Palmenberg AC. Conservation of the putative receptor attachment site in picornaviruses. Virology. 1988 Jun;164(2):373-82.PMID:2835857 DOI:10.1016/0042-6822(88)90550-8