View source: R/calculate_physicochemical_properties.R
calculate_physicochemical_properties | R Documentation |
Peptides
libraryCalculate EMBOSS-inspired theoretical physicochemical properties and rates using the Peptides
library
calculate_physicochemical_properties(seqs)
seqs |
A character vector with protein sequences or an object that can be coerced to that. |
A DataFrame
This documentation is based on the following documentation: https://github.com/dosorio/Peptides/
molecular.weight
: sum of the masses of each atom constituting a
molecule (Da) using the same formulas and weights as ExPASy's.
charge
: net charge of a protein sequence based on the
Henderson-Hasselbalch equation using Lehninger pKa scale.
pI
: isoelectric point calculated as in EMBOSS PEPSTATS.
mz
: mass over charge ratio (m/z) for peptides, as measured in mass spectrometry.
aIndex
: aliphatic index of a protein. The aindex is defined as the
relative volume occupied by aliphatic side chains (Alanine, Valine,
Isoleucine, and Leucine). It may be regarded as a positive factor
for the increase of thermostability of globular proteins.
boman
: potential protein interaction index . The index is equal to the
sum of the solubility values for all residues in a sequence, it might give
an overall estimate of the potential of a peptide to bind to membranes or
other proteins as receptors, to normalize it is divided by the number of
residues. A protein have high binding potential if the index value is
higher than 2.48.
hydrophobicity
: GRAVY hydrophobicity index of an amino acids sequence using
KyteDoolittle hydophobicity scale.
instaIndex
: Guruprasad's instability index. This index predicts the stability
of a protein based on its amino acid composition, a protein whose instability
index is smaller than 40 is predicted as stable, a value above 40 predicts
that the protein may be unstable.
STYNQW
: Percentage of amino acids (S + T + Y + N + Q + W)
Tiny
: Percentage of amino acids (A + C + G + S + T)
Small
: Percentage of amino acids (A + B + C + D + G + N + P + S + T + V)
Aliphatic
: Percentage of amino acids (A + I + L + V)
Aromatic
: Percentage of amino acids (F + H + W + Y)
Non-polar
: Percentage of amino acids (A + C + F + G + I + L + M + P + V + W + Y)
Polar
: Percentage of amino acids (D + E + H + K + N + Q + R + S + T + Z)
Charged
: Percentage of amino acids (B + D + E + H + K + R + Z)
Basic
: Percentage of amino acids (H + K + R)
Acidic
: Percentage of amino acids (B + D + E + Z)
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