boman {Peptides}

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