hydrophobicity_plot: hydrophobicity_plot

In Fiscore: Effective Protein Structural Data Visualisation and Exploration

Description

Function to plot amino acid sequence hydrophobicity profile using Kyte-Doolittle hydrophobicity scale; Reference= J. Mol. Biol. 157=105-132;1982. The Kyte-Doolittle scale is used for detecting hydrophobic regions in proteins. Regions with a positive value are hydrophobic ans those with negative values are hydrophylic. This scale can be used to identify both surface-exposed regions as well as transmembrane regions, depending on the window size used.

Usage

hydrophobicity_plot(pdb_df, window = 3, weight = 100, model = "exponential")

Arguments

pdb_df	Requires a pdb data frame generated by PDB_prepare
window	Size of a window between 3 and 21, default is 21
weight	Relative weight of the window edges compared to the window center in percent; default=100
model	Weight variation model either "linear" or "exponential", if the relative weight at the edges is selected to be < 100 percent; default="linear"

Value

Scaled line graph

Examples

path_to_processed_PDB<- system.file("extdata", "pdb_df.tabular", package="Fiscore")
# basic usage of hydrophobicity_plot
pdb_df<-read.table(path_to_processed_PDB)
hydrophobicity_plot(pdb_df)

Fiscore documentation built on Sept. 5, 2021, 5:51 p.m.