Peptides

R package to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot ‘XVG’ 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
aaDescriptors Compute 66 descriptors for each amino acid 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
blosumIndices Compute the BLOSUM62 derived indices 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
fasgaiVectors Compute the FASGAI vectors of a protein sequence
hmoment Compute the hydrophobic moment of a protein sequence
hydrophobicity Compute the hydrophobicity index of a protein sequence
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
mswhimScores Compute the MS-WHIM scores of a protein sequence
mw Compute the molecular weight of a protein sequence
pI Compute the isoelectic point (pI) of a protein sequence
plotXVG Plot time series from GROMACS XVG files
protFP Compute the protFP descriptors of a protein sequence
readXVG Read XVG files from GROMACS molecular dynamics package
stScales Compute the ST-scales of a protein sequence
tScales Compute the T-scales of a protein sequence
vhseScales Compute the VHSE-scales of a protein sequence
zScales Compute the Z-scales of a protein sequence

Available datasets

Code Description
AAdata Properties, scales and indices for the 20 naturally occurring amino acids from various sources
pepdata A data frame with 21 physicochemical properties and indices from 100 amino-acid sequences (50 antimicrobial and 50 non antimicrobial)

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 2.2.