Description Usage Arguments Value Examples
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
1 | assign_params(mypdb)
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mypdb |
This is an object given by a .pdb file process by both Rpdb and pdb_dataframe() |
This function returns another dataframe with logP and acidity parameters by residue
1 2 3 4 5 6 | library(Rpdb)
library(tidyverse)
library(dplyr)
y <- pdb_dataframe(CYP)
z <- assign_params(y)
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