Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

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Documentation for package ‘Peptides’ version 2.4.6

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aaComp Compute the amino acid composition of a protein sequence
AAdata Properties, scales and indices for the 20 naturally occurring amino acids from various sources
aaDescriptors Compute 66 descriptors for each amino acid of a protein sequence.
aaList Return a vector with the 20 standard amino acids in upper case
aaSMILES Create Smiles String from aminoacid sequences
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
massShift Calculate the mass difference of modified peptides.
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
mz Calculate the m/z for peptides.
pepdata Physicochemical properties and indices from 100 amino acid sequences
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