Peptides (version 1.0.1)

aindex: Compute the aliphatic index of a protein sequence

Description

This function calculates the Ikai (1980) 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.

Usage

aindex(seq)

Arguments

seq

amino acid sequence string in upper case

References

Ikai (1980). Thermostability and aliphatic index of globular proteins. Journal of Biochemistry, 88(6), 1895-1898.

Examples

# COMPARED TO ExPASy ALIPHATIC INDEX
# http://web.expasy.org/protparam/
  
# SEQUENCE: SDKEVDEVDAALSDLEITLE
# Aliphatic index: 117.00
  
aindex("SDKEVDEVDAALSDLEITLE")
# [1] 117