Peptides (version 1.1.0)

kidera: Compute the Kidera factors

Description

The Kidera Factors were originally derived by applying multivariate analysis to 188 physical properties of the 20 amino acids and using dimension reduction techniques. This function calculates the average of a factor using one of the ten Kidera factors.

Usage

kidera(seq,factor)

Arguments

seq

amino acid sequence string in upper case

factor

a character string specifying the Kidera factor to be used; must be one of "helix.bend.pref", "side.chain.size", "extended.str.pref", "hydrophobicity", "double.bend.pref", "partial.spe

References

Kidera, A., Konishi, Y., Oka, M., Ooi, T., & Scheraga, H. A. (1985). Statistical analysis of the physical properties of the 20 naturally occurring amino acids. Journal of Protein Chemistry, 4(1), 23-55.

Examples

kidera(seq = "KLKLLLLLKLK", factor = "helix.bend.pref")
# [1] -0.7854545

kidera(seq = "KLKLLLLLKLK", factor = "side.chain.size")
# [1] 0.2981818

kidera(seq = "KLKLLLLLKLK", factor = "extended.str.pref")
# [1] -0.2363636

kidera(seq = "KLKLLLLLKLK", factor = "hydrophobicity")
# [1] -0.08181818

kidera(seq = "KLKLLLLLKLK", factor = "double.bend.pref")
# [1] 0.21

kidera(seq = "KLKLLLLLKLK", factor = "partial.spec.vol")
# [1] -1.893636

kidera(seq = "KLKLLLLLKLK", factor = "flat.ext.pref")
# [1] 1.029091

kidera(seq = "KLKLLLLLKLK", factor = "occurrence.alpha.reg")
# [1] -0.5127273

kidera(seq = "KLKLLLLLKLK", factor = "pK.C")
# [1] 0.1118182

kidera(seq = "KLKLLLLLKLK", factor = "surrounding.hydrop")
# [1] 0.81