PyRoShift (PYthon ROtamers from chemical SHIFT) is a module that calculates protein side-chain rotamer populations from carbon chemical shifts. Currently it is implemented for isoleucine. If you want to add another residue please get in touch!
If you use this program please cite the following:
Determining isoleucine side-chain rotamer-sampling in proteins from 13C chemical shift.
Siemons L, Uluca-Yazgi B, Pritchard RB, McCarthy S, Heise H, Hansen F.
ChemCom 2019;
DOI: 10.1039/C9CC06496F
Site: https://pubs.rsc.org/en/Content/ArticleLanding/2019/CC/C9CC06496F#!divAbstract
Principally this method takes the isoleucine 13C chemical shifts (Ca, Cb, Cg1, Cg2 and Cd1) and determines the population for each of the four rotamers:
- t/t
- m/m
- p/t
- m/t
Where:
- t = trans (180 degrees)
- m = gauche - (300 degrees)
- p = gauche + ( 60 degrees)
Unlike many other methods this approach considers each rotamer to be defined by both chi angles! The first letter denotes the state of chi 1 and the second the state of chi 2.
On Linux and Mac one can install this module as with any other module. To do this follow these steps:
- Download this repository from the github page. (https://github.com/L-Siemons/PyRoShift)
- Go to the directory where the setup.py is
- Install as follows:
$ python setup.py build
$ python setup.py install
or
pip install .
Note that depending on how your system is set up you might need to use sudo.
For an example on how to use this module please see the example_run/ directory. Here there should be an example called run.py and also a ipython notebook describing all the steps. Sometimes the notebook doesn't render properly on github so I have also exported it as an html file that can be opened in a browser.
Sometimes the Ipython Notebook does not render correctly in the github page. If this happens the Notebook can be viewed at
https://nbviewer.jupyter.org/github/L-Siemons/PyRoShift/blob/master/example_run/Tutorial.ipynb
To run the example script simply use
python run.py
This module is written and maintained by Lucas Siemons
If you have any question please feel free to email me at [email protected].
On a more personal note this is my first Python module and if you have any critical advice on how to improve this body of code (both functionally and stylistically) please let me know!