boman: Compute the Boman (Potential Protein Interaction) index

In Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Compute the Boman (Potential Protein Interaction) index

Description

This function computes the potential protein interaction index proposed by Boman (2003) based in the amino acid sequence of a protein. 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.

Usage

boman(seq)

Arguments

seq	An amino-acid sequence

Details

The potential protein interaction index was proposed by Boman (2003) as an easy way to differentiate the action mechanism of hormones (protein-protein) and antimicrobial peptides (protein-membrane) through this index. This function predicts the potential peptide interaction with another protein.

Value

The computed potential protein-protein interaction for a given amino-acids sequence

References

Boman, H. G. (2003). Antibacterial peptides: basic facts and emerging concepts. Journal of Internal Medicine, 254(3), 197-215.

Examples

# COMPARED TO YADAMP DATABASE
# http://yadamp.unisa.it/showItem.aspx?yadampid=845&x=0,4373912
# SEQUENCE: FLPVLAGLTPSIVPKLVCLLTKKC
# BOMAN INDEX  -1.24  

boman(seq= "FLPVLAGLTPSIVPKLVCLLTKKC")
# [1] -1.235833

Peptides documentation built on May 29, 2024, 11:02 a.m.