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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

CodeFunction
aaListReturn a vector with the 20 standard aminoacids in upper case
aaCompCompute the amino-acid composition of a protein sequence
aaDescriptorsCompute 66 descriptors for each amino acid of a protein sequence
aIndexCompute the aliphatic index of a protein sequence
autoCorrelationCompute the auto-correlation index of a protein sequence
autoCovarianceCompute the auto-covariance index of a protein sequence
blosumIndicesCompute the BLOSUM62 derived indices of a protein sequence
bomanCompute the Boman (Potential Protein Interaction) index
chargeCompute the theoretical net charge of a protein sequence
crossCovarianceCompute the cross-covariance index of a protein sequence
crucianiPropertiesCompute the Cruciani properties of a protein sequence
fasgaiVectorsCompute the FASGAI vectors of a protein sequence
hmomentCompute the hydrophobic moment of a protein sequence
hydrophobicityCompute the hydrophobicity index of a protein sequence
instaIndexCompute the instability index of a protein sequence
kideraFactorsCompute the Kidera factors of a protein sequence
lengthpepCompute the aminoacid length of a protein sequence
massShiftCompute the mass difference of a protein sequence labelled with stable isotope.
membposCompute theoretically the class of a protein sequence
mswhimScoresCompute the MS-WHIM scores of a protein sequence
mwCompute the molecular weight of a protein sequence
mzCompute the mass over charge (m/z) of a protein sequence
pICompute the isoelectic point (pI) of a protein sequence
plotXVGPlot time series from GROMACS XVG files
protFPCompute the protFP descriptors of a protein sequence
readXVGRead XVG files from GROMACS molecular dynamics package
stScalesCompute the ST-scales of a protein sequence
tScalesCompute the T-scales of a protein sequence
vhseScalesCompute the VHSE-scales of a protein sequence
zScalesCompute the Z-scales of a protein sequence

Available datasets

CodeDescription
AAdataProperties, scales and indices for the 20 naturally occurring amino acids from various sources
pepdataA 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).

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Version

Install

install.packages('Peptides')

Monthly Downloads

1,047

Version

2.4.6

License

GPL-2

Issues

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Stars

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Maintainer

Last Published

December 13th, 2023

Functions in Peptides (2.4.6)

crucianiProperties

Compute the Cruciani properties of a protein sequence
fasgaiVectors

Compute the FASGAI vectors of a protein sequence
pI

Compute the isoelectic point (pI) of a protein sequence
massShift

Calculate the mass difference of modified peptides.
pepdata

Physicochemical properties and indices from 100 amino acid sequences
hmoment

Compute the hydrophobic moment of a protein sequence
hydrophobicity

Compute the hydrophobicity index of a protein sequence
zScales

Compute the Z-scales of a protein sequence
plotXVG

Plot time series from GROMACS XVG files
protFP

Compute the protFP descriptors of a protein sequence
kideraFactors

Compute the Kidera factors of a protein sequence
instaIndex

Compute the instability index of a protein sequence
vhseScales

Compute the VHSE-scales of a protein sequence
tScales

Compute the T-scales of a protein sequence
mw

Compute the molecular weight of a protein sequence
membpos

Compute theoretically the class of a protein sequence
readXVG

Read output data from a XVG format file.
stScales

Compute the ST-scales of a protein sequence
mswhimScores

Compute the MS-WHIM scores of a protein sequence
mz

Calculate the m/z for peptides.
aIndex

Compute the aliphatic index of a protein sequence
autoCovariance

Compute the auto-covariance index of a protein sequence
aaList

Return a vector with the 20 standard amino acids in upper case
blosumIndices

Compute the BLOSUM62 derived indices of a protein sequence
boman

Compute the Boman (Potential Protein Interaction) index
aaComp

Compute the amino acid composition of a protein sequence
autoCorrelation

Compute the auto-correlation index of a protein sequence
aaDescriptors

Compute 66 descriptors for each amino acid of a protein sequence.
aaSMILES

Create Smiles String from aminoacid sequences
AAdata

Properties, scales and indices for the 20 naturally occurring amino acids from various sources
charge

Compute the theoretical net charge of a protein sequence
lengthpep

Compute the amino acid length of a protein sequence
crossCovariance

Compute the cross-covariance index of a protein sequence