OPM is a program to predict the location of transmembrane planes in protein structures, utilizing the atomic coordinates. ssbio provides a wrapper to submit PDB files to the web server, cache, and parse the results.
- Use the function
ssbio.protein.structure.properties.opm.run_ppm_server()to upload a PDB file to the PPM server.
How can I install OPM?
- OPM is only available as a web server. ssbio provides a wrapper for the web server and allows you to submit protein structures to it along with caching the output files.
How do I cite OPM?
- Lomize MA, Pogozheva ID, Joo H, Mosberg HI & Lomize AL (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res. 40: D370–6 Available at: http://dx.doi.org/10.1093/nar/gkr703
I’m having issues running OPM…
- See the ssbio wiki for (hopefully) some solutions - or add yours in when you find the answer!
run_ppm_server(pdb_file, outfile, force_rerun=False)¶
Run the PPM server from OPM to predict transmembrane residues.
- pdb_file (str) – Path to PDB file
- outfile (str) – Path to output HTML results file
- force_rerun (bool) – Flag to rerun PPM if HTML results file already exists
Dictionary of information from the PPM run, including a link to download the membrane protein file