get.area()

Description

Computes Online Surface Energies Using the Getarea Server

Usage

get.area(pdb, keepfiles = FALSE)

Arguments

pdb is either a PDB id, or the path to a pdb file.

keepfiles logical, if TRUE the dataframe will be saved in the working directory and we will keep the getarea txt file.

Value

This function returns a dataframe containing the requested information.

References

Details

Analysis of protein commonly requires the partition of their structure into regions such as the surface, interior, or interface. Whenever you are interested into analysing such a partition in a particular protein, the following function of the ptm package may be of help:

The function get.area() returns the surface energies computed as described by Fraczkiewicz & Braun. Further details can be obtained here.

Using as example the human hexokinase 1, which is a monomeric protein, the output of the current function would look something like this:

hHK1 <- get.area(pdb = '1cza')
kable(head(hHK1))

elenoeletyresidresnoareaenergy
1ND1635.61
2CAD166.26
3CD160.00
4OD160.00
5CBD1617.58
6CGD161.75