Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Includes functions 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 the latest version of this package by entering the following in R:
install.packages("Peptides")
AuthorDaniel Osorio [aut, cre], Paola Rondon-Villarreal [aut, ths], Rodrigo Torres [aut, ths], J. Sebastian Paez [ctb]
Date of publication2017-03-12 22:24:31
MaintainerDaniel Osorio <dcosorioh@unal.edu.co>
LicenseGPL-2
Version2.0.0
https://github.com/dosorio/Peptides/

View on CRAN

Man pages

aaComp: Compute the amino acid composition of a protein sequence

AAdata: Properties, scales and indices for the 20 naturally occurring...

aaDescriptors: Compute 66 descriptors for each amino acid of a protein...

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 amino acid 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

pepdata: Physicochemical properties and indices from 100 amino acid...

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 output data from a XVG format file.

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

Functions

aaComp Man page
AAdata Man page
aaDescriptors Man page
aIndex Man page
autoCorrelation Man page
autoCovariance Man page
blosumIndices Man page
boman Man page
charge Man page
crossCovariance Man page
crucianiProperties Man page
fasgaiVectors Man page
hmoment Man page
hydrophobicity Man page
instaIndex Man page
kideraFactors Man page
lengthpep Man page
membpos Man page
mswhimScores Man page
mw Man page
pepdata Man page
pI Man page
plotXVG Man page
protFP Man page
readXVG Man page
stScales Man page
tScales Man page
vhseScales Man page
zScales Man page

Files

inst
inst/CITATION
inst/xvg-files
inst/xvg-files/RDF.xvg
inst/xvg-files/POPC.xvg
inst/xvg-files/POPG.xvg
inst/xvg-files/POPE.xvg
inst/xvg-files/epot.xvg
tests
tests/testthat.R
tests/testthat
tests/testthat/test.hmoment.R tests/testthat/test.hydrophobicity.R tests/testthat/test.boman.R tests/testthat/test.pI.R tests/testthat/test.lengthpep.R tests/testthat/test.aindex.R tests/testthat/test.mw.R tests/testthat/test.instaindex.R tests/testthat/test.charge.R tests/testthat/test.aacomp.R
NAMESPACE
NEWS.md
data
data/AAdata.RData
data/pepdata.RData
data/datalist
R
R/data-pepdata.R R/protFP.R R/zScales.R R/lengthpep.R R/boman.R R/stScales.R R/blosumIndices.R R/membpos.R R/aaDescriptors.R R/autocorrelation.R R/crucianiProperties.R
R/sysdata.rda
R/plotXVG.R R/tScales.R R/aaCheck.R R/crosscovariance.R R/kideraFactors.R R/fasgaiVectors.R R/mw.R R/pI.R R/hmoment.R R/autocovariance.R R/aacomp.R R/vhseScales.R R/readXVG.R R/hydrophobicity.R R/charge.R R/mswhimScores.R R/aindex.R R/instaindex.R R/data-AA.R
README.md
MD5
DESCRIPTION
man
man/lengthpep.Rd man/mswhimScores.Rd man/protFP.Rd man/crucianiProperties.Rd man/aaComp.Rd man/mw.Rd man/plotXVG.Rd man/pepdata.Rd man/charge.Rd man/tScales.Rd man/instaIndex.Rd man/crossCovariance.Rd man/hydrophobicity.Rd man/fasgaiVectors.Rd man/zScales.Rd man/AAdata.Rd man/blosumIndices.Rd man/aIndex.Rd man/membpos.Rd man/vhseScales.Rd man/hmoment.Rd man/pI.Rd man/autoCovariance.Rd man/autoCorrelation.Rd man/boman.Rd man/aaDescriptors.Rd man/readXVG.Rd man/stScales.Rd man/kideraFactors.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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