Peptides (version 0.4)

boman: To calculate the Boman (Potential Protein Interaction) Index

Description

Calculate the protein binding potential using a published thermodynamics solubility properties for amino acid side chains. The index is equal to the sum of the solubility values for all residues in a sequence might give an overall estimate of the potential of a peptide to bind to membranes or other proteins such as different receptors, to normalize it is divided by the number of residues.

Usage

boman(seq)

Arguments

seq

AA sequence string in upper case

Value

• The Boman index as a numerical vector of length one

Details

Protein have high binding potential if the index value is higher than 2.48 (Boman, 2003)

References

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

Radzicka, A., & Wolfenden, R. (1988). Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry, 27(5), 1664-1670.

Examples

boman("GIGKFLHSAKKFGKAFVGEIMNS")

##Output
# [1] 0.42