Peptides
R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences. Include also the option to read and plot output files from the GROMACS molecular dynamics package.
Install
This package required R version 1.2.2 or higher. If you are using an older version of R you will be prompted to upgrade when you try to install the package.
The official release of Peptides is available on CRAN. To install from CRAN, use the following command:
install.packages("Peptides", dependencies=TRUE)If you have devtools installed, install the latest stable version this package directly from GitHub:
library(devtools)
install_github("dosorio/Peptides")
library(Peptides)Available functions
| Code | Function |
|---|---|
| aacomp | Compute the amino-acid composition of a protein sequence |
| aindex | Compute the aliphatic index of a protein sequence |
| autoCorrelation | Compute the auto-correlation index of a protein sequence |
| autoCovariance | Compute the auto-covariance index of a protein sequence |
| boman | Compute the Boman (Potential Protein Interaction) index |
| charge | Compute the theoretical net charge of a protein sequence |
| crossCovariance | Compute the cross-covariance index of a protein sequence |
| crucianiProperties | Compute the Cruciani properties of a protein sequence |
| hmoment | Compute the hydrophobic moment of a protein sequence |
| hydrophobicity | Compute the hydrophobicity index |
| instaindex | Compute the instability index of a protein sequence |
| kideraFactors | Compute the Kidera factors of a protein sequence |
| lengthpep | Compute the aminoacid length of a protein sequence |
| membpos | Compute theoretically the class of a protein sequence |
| mw | Compute the molecular weight of a protein sequence |
| pI | Compute the isoelectic point (pI) of a protein sequence |
| plot.xvg | Plot time series from GROMACS XVG files |
| read.xvg | Read XVG files from GROMACS molecular dynamics package |
Available datasets
| Code | Description |
|---|---|
| CP | The 3 properties from Cruciani et. al (2004) |
| H | 38 Hydrophobicity values for amino acids form various sources |
| K | The 10 factors from Kidera et. al (1985) |
| pepdata | A data frame with 21 physicochemical properties and indices from 100 amino-acid sequences (50 antimicrobial and 50 non antimicrobial) |
| pK | 9 pKa scales for the side chain of charged amino acids from various sources |
Citation
Osorio, D., Rondon-Villarreal, P. & Torres, R. Peptides: A package for data mining of antimicrobial peptides. The R Journal. 7(1), 4–14 (2015).
D. Osorio, P. Rondón-Villarreal and R. Torres. Peptides: Calculate indices and theoretical physicochemical properties of peptides and protein sequences., 2014. URL: http: //CRAN.R-project.org/package=Peptides. R Package Version 1.2.1.