https://github.com/normcyr/monolayers-binding-parameters
R script to calculate the binding parameters (and corresponding errors) MIP and synergy of proteins upon binding to lipid monolayers.
https://github.com/normcyr/monolayers-binding-parameters
Last synced: about 2 months ago
JSON representation
R script to calculate the binding parameters (and corresponding errors) MIP and synergy of proteins upon binding to lipid monolayers.
- Host: GitHub
- URL: https://github.com/normcyr/monolayers-binding-parameters
- Owner: normcyr
- Created: 2017-12-15T20:20:57.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2017-12-17T06:56:05.000Z (over 7 years ago)
- Last Synced: 2025-02-14T23:38:50.439Z (4 months ago)
- Language: R
- Size: 18.6 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# R script to calculate binding parameters in monolayer experiments
## Description
This repository offer a complementory R script to a scientific paper which will soon be published (currently pending review - reference will be added accordingly). The goal of this script is to facilitate the calculation of binding parameters (and corresponding errors) associated with Langmuir monolayers experiments.
## How to use it
You can either clone the git repository locally or simply download the R script file named `binding-parameters-calculations.R`.
Then, using your preferred R interpreter (*eg* [RStudio](https://github.com/rstudio/rstudio); a more exhaustive list can be found [here](https://en.wikipedia.org/wiki/R_programming_language#Interfaces)), open the R script.
We provide you with an example data set (`example-data.csv`) which can also be downloaded and used as trial data. The first column has to be Πi data and the second column ΔΠ data.
Your data has to be provided as a `csv` file where the first line corresponds to headers. Alternatively, you may modify the R script to suit your data format.
The script will read your data and generate a ΔΠ vs Πi plot like the following:
![alt text][plot]
The authors do not pretend to great artistic talent. You are therefore encouraged to modify the resulting plot to your needs and artistic capabilities. R offers various packages for plot generation.
## References and further readings
References for the calculations:
- Calvez *et al*. (2009) *Biochimie* 91:718. ([Pubmed](https://www.ncbi.nlm.nih.gov/pubmed/19345719))
- Calvez *et al*. (2011) *Langmuir* 27:1373. ([Pubmed](https://www.ncbi.nlm.nih.gov/pubmed/21210634))
- Boisselier *et al*. (2017) *Advances in Colloid and Interface Science* 243:60. ([Pubmed](https://www.ncbi.nlm.nih.gov/pubmed/28372794))
A web server offering similar features is available [here](http://www.crchudequebec.ulaval.ca/BindingParametersCalculator/).
[plot]: https://normcyr.github.io/img/example-plot.svg "Example plot generated by the R script"