assign_params: Add the chemical properties to the tibble of coordinates for...

In zalperst/visualizeprot: Visualize the Protein Chemical Property Landscape

Description

The parameters used for amino acid assignment are shown below, with the reference given at the bottom. LogP values are calculated. Assign logP, acidic/basic/neutral R,-4.2,Acidic K,-3.05,Basic D,-3.89,Acidic N,-3.82,Neutral E,-3.69,Acidic Q,-3.64,Neutral H,-3.32,Basic P,-2.54,Neutral Y,-2.26,Neutral W,-1.05,Neutral S,-3.07,Neutral T,-2.94,Neutral G,-3.21,Neutral A,-2.85,Neutral M,-1.87,Neutral C,-2.49,Neutral F,-1.38,Neutral L,-1.52,Neutral V,-2.26,Neutral I,-1.70,Neutral http://www2d.biglobe.ne.jp/~chem_env/amino/amino2j_e.html

Usage

assign_params(mypdb)

Arguments

mypdb

This is an object given by a .pdb file process by both Rpdb and pdb_dataframe()

Value

This function returns another dataframe with logP and acidity parameters by residue

Examples

library(Rpdb)
library(tidyverse)
library(dplyr)

y <- pdb_dataframe(CYP)
z <- assign_params(y)

zalperst/visualizeprot documentation built on May 4, 2019, 9:08 p.m.