Peptides: Calculate Indices and Theoretical Properties of Protein Sequences

Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot output files from the 'GROMACS' molecular dynamics package.

Author
Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
Date of publication
2015-11-27 08:53:11
Maintainer
Daniel Osorio <daniel.osorio@correo.uis.edu.co>
License
GPL-2
Version
1.1.1
URLs

View on CRAN

Man pages

aacomp
Compute the amino acid composition of a protein sequence
aindex
Compute the aliphatic index of a protein sequence
boman
Compute the Boman (Potential Protein Interaction) index
charge
Compute the theoretical net charge of a protein sequence
h
38 Hydrophobicity values for amino acids from various sources
hmoment
Compute the hydrophobic moment of a protein sequence
hydrophobicity
Compute the hydrophobicity index
instaindex
Compute the instability index of a protein sequence
Kfactors
The Ten Kidera Factors
kidera
Compute the Kidera factors
lengthpep
Compute the amino acid length of a protein sequence
membpos
Compute theoretically the class of a protein sequence
mw
Compute the molecular weight of a protein sequence
pepdata
Physicochemical properties and indices from 100 amino acid...
Peptides-package
Calculate Indices and Theoretical Properties of Protein...
pI
Compute the isoelectic point (pI) of a protein sequence
pKscales
9 pKa scales for the side chain of charged amino acids from...
plot.xvg
Plot time series from GROMACS XVG files
read.xvg
Read XVG files from GROMACS Molecular Dynamics package

Files in this package

Peptides
Peptides/inst
Peptides/inst/tests
Peptides/inst/tests/runit.lengthpep.R
Peptides/inst/tests/runit.aacomp.R
Peptides/inst/tests/runit.boman.R
Peptides/inst/tests/runit.pI.R
Peptides/inst/tests/runalltest.R
Peptides/inst/tests/runit.hydrophobicity.R
Peptides/inst/tests/runit.aindex.R
Peptides/inst/tests/runit.mw.R
Peptides/inst/tests/runit.instaindex.R
Peptides/inst/tests/runit.hmoment.R
Peptides/inst/tests/runit.charge.R
Peptides/inst/xvg-files
Peptides/inst/xvg-files/POPC.xvg
Peptides/inst/xvg-files/POPG.xvg
Peptides/inst/xvg-files/POPE.xvg
Peptides/inst/xvg-files/epot.xvg
Peptides/tests
Peptides/tests/doRUnit.R
Peptides/NAMESPACE
Peptides/NEWS
Peptides/data
Peptides/data/H.RData
Peptides/data/Kfactors.RData
Peptides/data/pepdata.RData
Peptides/data/datalist
Peptides/data/pKscales.RData
Peptides/R
Peptides/R/lengthpep.R
Peptides/R/boman.R
Peptides/R/membpos.R
Peptides/R/plot.xvg.R
Peptides/R/kidera.R
Peptides/R/mw.R
Peptides/R/pI.R
Peptides/R/hmoment.R
Peptides/R/aacomp.R
Peptides/R/read.xvg.R
Peptides/R/hydrophobicity.R
Peptides/R/charge.R
Peptides/R/aindex.R
Peptides/R/instaindex.R
Peptides/MD5
Peptides/DESCRIPTION
Peptides/man
Peptides/man/lengthpep.Rd
Peptides/man/pKscales.Rd
Peptides/man/mw.Rd
Peptides/man/h.Rd
Peptides/man/pepdata.Rd
Peptides/man/charge.Rd
Peptides/man/aacomp.Rd
Peptides/man/read.xvg.Rd
Peptides/man/instaindex.Rd
Peptides/man/hydrophobicity.Rd
Peptides/man/Kfactors.Rd
Peptides/man/kidera.Rd
Peptides/man/Peptides-package.Rd
Peptides/man/membpos.Rd
Peptides/man/hmoment.Rd
Peptides/man/pI.Rd
Peptides/man/boman.Rd
Peptides/man/plot.xvg.Rd
Peptides/man/aindex.Rd